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Liu Y, Lian G, Chen T. A novel multi-omics data analysis of dose-dependent and temporal changes in regulatory pathways due to chemical perturbation: a case study on caffeine. Toxicol Mech Methods 2024; 34:164-175. [PMID: 37794615 DOI: 10.1080/15376516.2023.2265462] [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: 07/19/2023] [Accepted: 09/26/2023] [Indexed: 10/06/2023]
Abstract
Comprehensive analysis of multi-omics data can reveal alterations in regulatory pathways induced by cellular exposure to chemicals by characterizing biological processes at the molecular level. Data-driven omics analysis, conducted in a dose-dependent or dynamic manner, can facilitate comprehending toxicity mechanisms. This study introduces a novel multi-omics data analysis designed to concurrently examine dose-dependent and temporal patterns of cellular responses to chemical perturbations. This analysis, encompassing preliminary exploration, pattern deconstruction, and network reconstruction of multi-omics data, provides a comprehensive perspective on the dynamic behaviors of cells exposed to varying levels of chemical stimuli. Importantly, this analysis is adaptable to any number of omics layers, including site-specific phosphoproteomics. We implemented this analysis on multi-omics data obtained from HepG2 cells exposed to a range of caffeine doses over varying durations and identified six response patterns, along with their associated biomolecules and pathways. Our study demonstrates the effectiveness of the proposed multi-omics data analysis in capturing multidimensional patterns of cellular response to chemical perturbation, enhancing understanding of pathway regulation for chemical risk assessment.
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Affiliation(s)
- Yufan Liu
- School of Chemistry and Chemical Engineering, University of Surrey, Guildford, UK
| | - Guoping Lian
- School of Chemistry and Chemical Engineering, University of Surrey, Guildford, UK
- Unilever R&D Colworth, Bedford, UK
| | - Tao Chen
- School of Chemistry and Chemical Engineering, University of Surrey, Guildford, UK
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2
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Targeted Quantification of Protein Phosphorylation and Its Contributions towards Mathematical Modeling of Signaling Pathways. Molecules 2023; 28:molecules28031143. [PMID: 36770810 PMCID: PMC9919559 DOI: 10.3390/molecules28031143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 01/12/2023] [Accepted: 01/18/2023] [Indexed: 01/26/2023] Open
Abstract
Post-translational modifications (PTMs) are key regulatory mechanisms that can control protein function. Of these, phosphorylation is the most common and widely studied. Because of its importance in regulating cell signaling, precise and accurate measurements of protein phosphorylation across wide dynamic ranges are crucial to understanding how signaling pathways function. Although immunological assays are commonly used to detect phosphoproteins, their lack of sensitivity, specificity, and selectivity often make them unreliable for quantitative measurements of complex biological samples. Recent advances in Mass Spectrometry (MS)-based targeted proteomics have made it a more useful approach than immunoassays for studying the dynamics of protein phosphorylation. Selected reaction monitoring (SRM)-also known as multiple reaction monitoring (MRM)-and parallel reaction monitoring (PRM) can quantify relative and absolute abundances of protein phosphorylation in multiplexed fashions targeting specific pathways. In addition, the refinement of these tools by enrichment and fractionation strategies has improved measurement of phosphorylation of low-abundance proteins. The quantitative data generated are particularly useful for building and parameterizing mathematical models of complex phospho-signaling pathways. Potentially, these models can provide a framework for linking analytical measurements of clinical samples to better diagnosis and treatment of disease.
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3
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Invergo BM. Accurate, high-coverage assignment of in vivo protein kinases to phosphosites from in vitro phosphoproteomic specificity data. PLoS Comput Biol 2022; 18:e1010110. [PMID: 35560139 PMCID: PMC9132282 DOI: 10.1371/journal.pcbi.1010110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 05/25/2022] [Accepted: 04/15/2022] [Indexed: 12/03/2022] Open
Abstract
Phosphoproteomic experiments routinely observe thousands of phosphorylation sites. To understand the intracellular signaling processes that generated this data, one or more causal protein kinases must be assigned to each phosphosite. However, limited knowledge of kinase specificity typically restricts assignments to a small subset of a kinome. Starting from a statistical model of a high-throughput, in vitro kinase-substrate assay, I have developed an approach to high-coverage, multi-label kinase-substrate assignment called IV-KAPhE (“In vivo-Kinase Assignment for Phosphorylation Evidence”). Tested on human data, IV-KAPhE outperforms other methods of similar scope. Such computational methods generally predict a densely connected kinase-substrate network, with most sites targeted by multiple kinases, pointing either to unaccounted-for biochemical constraints or significant cross-talk and signaling redundancy. I show that such predictions can potentially identify biased kinase-site misannotations within families of closely related kinase isozymes and they provide a robust basis for kinase activity analysis. Proteins can pass around information inside cells about changes in the environment. This process, called intracellular signaling, helps to trigger appropriate cellular responses to environmental changes. One of the main ways information is passed to proteins is through chemical “tagging,” called phosphorylation, by enzymes called protein kinases. We can measure the phosphorylation state of practically all proteins in a cell at any moment. Starting from known cases of phosphorylation by a kinase, many computational methods have been developed to predict if the kinase might tag a certain spot on another protein or if an observed tag was attached by the kinase, with different models for each kinase. I have developed a new method that instead uses a single model to assign one or more kinases to each observed tag, built from the latest large-scale experimental data. This change in focus and unbiased training data allows my method to be significantly more accurate than past methods. I also explored useful applications for my method. For example, I used it to show that much of our knowledge about which kinase is responsible for each tag is probably inaccurately biased towards the commonly studied ones.
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Affiliation(s)
- Brandon M. Invergo
- Translational Research Exchange @ Exeter, University of Exeter, Exeter, United Kingdom
- * E-mail:
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4
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Substrates of the MAPK Slt2: Shaping Yeast Cell Integrity. J Fungi (Basel) 2022; 8:jof8040368. [PMID: 35448599 PMCID: PMC9031059 DOI: 10.3390/jof8040368] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 03/30/2022] [Accepted: 03/31/2022] [Indexed: 02/04/2023] Open
Abstract
The cell wall integrity (CWI) MAPK pathway of budding yeast Saccharomyces cerevisiae is specialized in responding to cell wall damage, but ongoing research shows that it participates in many other stressful conditions, suggesting that it has functional diversity. The output of this pathway is mainly driven by the activity of the MAPK Slt2, which regulates important processes for yeast physiology such as fine-tuning of signaling through the CWI and other pathways, transcriptional activation in response to cell wall damage, cell cycle, or determination of the fate of some organelles. To this end, Slt2 precisely phosphorylates protein substrates, modulating their activity, stability, protein interaction, and subcellular localization. Here, after recapitulating the methods that have been employed in the discovery of proteins phosphorylated by Slt2, we review the bona fide substrates of this MAPK and the growing set of candidates still to be confirmed. In the context of the complexity of MAPK signaling regulation, we discuss how Slt2 determines yeast cell integrity through phosphorylation of these substrates. Increasing data from large-scale analyses and the available methodological approaches pave the road to early identification of new Slt2 substrates and functions.
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Szydzik J, Lind DE, Arefin B, Kurhe Y, Umapathy G, Siaw JT, Claeys A, Gabre JL, Van den Eynden J, Hallberg B, Palmer RH. ATR inhibition enables complete tumour regression in ALK-driven NB mouse models. Nat Commun 2021; 12:6813. [PMID: 34819497 PMCID: PMC8613282 DOI: 10.1038/s41467-021-27057-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 11/03/2021] [Indexed: 01/23/2023] Open
Abstract
High-risk neuroblastoma (NB) often involves MYCN amplification as well as mutations in ALK. Currently, high-risk NB presents significant clinical challenges, and additional therapeutic options are needed. Oncogenes like MYCN and ALK result in increased replication stress in cancer cells, offering therapeutically exploitable options. We have pursued phosphoproteomic analyses highlighting ATR activity in ALK-driven NB cells, identifying the BAY1895344 ATR inhibitor as a potent inhibitor of NB cell growth and proliferation. Using RNA-Seq, proteomics and phosphoproteomics we characterize NB cell and tumour responses to ATR inhibition, identifying key components of the DNA damage response as ATR targets in NB cells. ATR inhibition also produces robust responses in mouse models. Remarkably, a 2-week combined ATR/ALK inhibition protocol leads to complete tumor regression in two independent genetically modified mouse NB models. These results suggest that NB patients, particularly in high-risk groups with oncogene-induced replication stress, may benefit from ATR inhibition as therapeutic intervention. Effective therapeutic options are still needed in neuroblastoma treatment. Here, the authors, through a comprehensive proteomics analysis, identify ATR as a potential therapeutic target of neuroblastoma and demonstrate the efficacy of the ATR inhibitor BAY1895344 in combination with the ALK tyrosine kinase inhibitor lorlatinib.
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Affiliation(s)
- Joanna Szydzik
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-40530, Gothenburg, Sweden
| | - Dan E Lind
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-40530, Gothenburg, Sweden
| | - Badrul Arefin
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-40530, Gothenburg, Sweden
| | - Yeshwant Kurhe
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-40530, Gothenburg, Sweden
| | - Ganesh Umapathy
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-40530, Gothenburg, Sweden
| | - Joachim Tetteh Siaw
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-40530, Gothenburg, Sweden
| | - Arne Claeys
- Department of Human Structure and Repair, Anatomy and Embryology Unit, Ghent University, 9000, Ghent, Belgium
| | - Jonatan L Gabre
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-40530, Gothenburg, Sweden.,Department of Human Structure and Repair, Anatomy and Embryology Unit, Ghent University, 9000, Ghent, Belgium
| | - Jimmy Van den Eynden
- Department of Human Structure and Repair, Anatomy and Embryology Unit, Ghent University, 9000, Ghent, Belgium.
| | - Bengt Hallberg
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-40530, Gothenburg, Sweden.
| | - Ruth H Palmer
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-40530, Gothenburg, Sweden.
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Liu X, Fields R, Schweppe DK, Paulo JA. Strategies for mass spectrometry-based phosphoproteomics using isobaric tagging. Expert Rev Proteomics 2021; 18:795-807. [PMID: 34652972 DOI: 10.1080/14789450.2021.1994390] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
INTRODUCTION Protein phosphorylation is a primary mechanism of signal transduction in cellular systems. Isobaric tagging can be used to investigate alterations in phosphorylation events in sample multiplexing experiments where quantification extends across all conditions. As such, innovations in tandem mass tag methods can facilitate the expansion of the depth and breadth of phosphoproteomic analyses. AREAS COVERED This review discusses the current state of tandem mass tag-centric phosphoproteomics and highlights advances in reagent chemistry, instrumentation, data acquisition, and data analysis. We stress that approaches for phosphoproteomic investigations require high-specificity enrichment, sensitive detection, and accurate phosphorylation site localization. EXPERT OPINION Tandem mass tag-centric phosphoproteomics will continue to be an important conduit for our understanding of signal transduction in living organisms. We anticipate that progress in phosphopeptide enrichment methodologies, enhancements in instrumentation and data acquisition technologies, and further refinements in analytical strategies will be key to the discovery of biologically relevant findings from phosphoproteomics studies.
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Affiliation(s)
- Xinyue Liu
- Department of Cell Biology, Harvard Medical School, Boston, USA
| | - Rose Fields
- Department of Genome Sciences, University of Washington, Seattle, USA
| | - Devin K Schweppe
- Department of Genome Sciences, University of Washington, Seattle, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, USA
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7
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Hu Z, Sankar DS, Vu B, Leytens A, Vionnet C, Wu W, Stumpe M, Martínez-Martínez E, Stork B, Dengjel J. ULK1 phosphorylation of striatin activates protein phosphatase 2A and autophagy. Cell Rep 2021; 36:109762. [PMID: 34592149 DOI: 10.1016/j.celrep.2021.109762] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 07/16/2021] [Accepted: 09/06/2021] [Indexed: 01/18/2023] Open
Abstract
The evolutionarily conserved ULK1 kinase complex acts as gatekeeper of canonical autophagy and regulates induction of autophagosome biogenesis. To better understand control of ULK1 and analyze whether ULK1 has broader functions that are also linked to the later steps of autophagy, we perform comprehensive phosphoproteomic analyses. Combining in vivo with in vitro data, we identify numerous direct ULK1 target sites within autophagy-relevant proteins that are critical for autophagosome maturation and turnover. In addition, we highlight an intimate crosstalk between ULK1 and several phosphatase complexes. ULK1 is not only a PP2A target but also directly phosphorylates the regulatory PP2A subunit striatin, activating PP2A and serving as positive feedback to promote autophagy-dependent protein turnover. Thus, ULK1 and phosphatase activities are tightly coordinated to robustly regulate protein degradation by autophagy.
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Affiliation(s)
- Zehan Hu
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
| | | | - Bich Vu
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
| | - Alexandre Leytens
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
| | - Christine Vionnet
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
| | - Wenxian Wu
- Institute of Molecular Medicine I, Medical Faculty, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Michael Stumpe
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
| | | | - Björn Stork
- Institute of Molecular Medicine I, Medical Faculty, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Jörn Dengjel
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland.
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8
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Sürmen MG, Sürmen S, Cansız D, Ünal İ, Üstündağ ÜV, Alturfan AA, Emekli-Alturfan E. Quantitative phosphoproteomics to resolve the cellular responses to octanoic acid in rotenone exposed zebrafish. J Food Biochem 2021; 45:e13923. [PMID: 34494670 DOI: 10.1111/jfbc.13923] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 07/29/2021] [Accepted: 08/20/2021] [Indexed: 01/02/2023]
Abstract
Ketosis is a potentially beneficial metabolic state for health especially in neurological conditions including Parkinson's disease (PD). Medium-chain-triglycerides (MCT) have specific metabolic properties and they are described as ketogenic even without restriction of carbohydrate. Octanoic acid (C8) is the main MCT showing this effect. Rotenone is a neurotoxin that is used to induce experimental PD model. Rotenone inhibits mitochondrial respiratory complex 1 (MRC1) and causes reactive oxygen species formation. Mass spectrometry (MS)-based phosphoproteomic methods enable discovering specific signaling events in special molecular pathways through identification and quantification of phosphoproteins. Signaling networks involved in rotenone-mediated biological processes and beneficial effects of MCTs on neurodegenerative diseases are not well understood. We aimed to gain comprehensive molecular perspective on the global phosphoproteome differences in rotenone-exposed zebrafish treated with octanoic acid. Raw files obtained from MS analysis were processed and searched against the Danio rerio protein database using SEQUEST-HT algorithm to identify and quantify phosphopeptides with 2,569 unique phosphoproteins and 4,161 unique phosphopeptides corresponding to 2005 proteins. Microtubule-associated protein (MAP) family members were significantly lower in rotenone group. Phosphoproteins involved in ion binding (calcium, magnesium, zinc ion), oxygen binding, microtubule binding, ATP- and GTP-binding were among differentially expressed 347 proteins in rotenone group and they were reversed after octanoic acid treatments. Phosphoproteins and phosphorylation sites were identified for future exploration of signaling pathways involved in rotenone toxicity. We believe our findings might help in the formulation of effective therapeutic strategies for the treatment of PD using ketogenic formulations involving MCTs. PRACTICAL APPLICATIONS: Ketosis is a potentially beneficial metabolic state for health especially in neurological conditions including Parkinson's disease (PD). Medium-chain-triglycerides (MCT) (C6-C12) have specific metabolic properties making them described as ketogenic even without restriction of carbohydrate. Octanoic acid (caprylic acid, C8) is the main MCT showing this effect. Our findings might help in the formulation of effective therapeutic strategies for the treatment of Parkinson's disease using ketogenic formulations involving Medium-chain-triglycerides.
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Affiliation(s)
- Mustafa Gani Sürmen
- Department of Molecular Medicine, Hamidiye Institute of Health Sciences, University of Health Sciences, Istanbul, Turkey
| | - Saime Sürmen
- Department of Molecular Medicine, Aziz Sancar Institute of Experimental Medicine, Istanbul University-Çapa, Istanbul, Turkey
| | - Derya Cansız
- Department of Biochemistry, Faculty of Medicine, Istanbul University-Cerrahpaşa, Istanbul, Turkey
| | - İsmail Ünal
- Department of Biochemistry, Institute of Health Sciences, Marmara University, Istanbul, Turkey
| | - Ünsal Veli Üstündağ
- Medical Biochemistry, Faculty of Medicine, Department Medipol University, Istanbul, Turkey
| | - Ahmet Ata Alturfan
- Department of Biochemistry, Faculty of Medicine, Istanbul University-Cerrahpaşa, Istanbul, Turkey
| | - Ebru Emekli-Alturfan
- Department of Basic Medical Sciences, Faculty of Dentistry, Marmara University, Istanbul, Turkey
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Low TY, Mohtar MA, Lee PY, Omar N, Zhou H, Ye M. WIDENING THE BOTTLENECK OF PHOSPHOPROTEOMICS: EVOLVING STRATEGIES FOR PHOSPHOPEPTIDE ENRICHMENT. MASS SPECTROMETRY REVIEWS 2021; 40:309-333. [PMID: 32491218 DOI: 10.1002/mas.21636] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 05/11/2020] [Accepted: 05/12/2020] [Indexed: 06/11/2023]
Abstract
Phosphorylation is a form of protein posttranslational modification (PTM) that regulates many biological processes. Whereas phosphoproteomics is a scientific discipline that identifies and quantifies the phosphorylated proteome using mass spectrometry (MS). This task is extremely challenging as ~30% of the human proteome is phosphorylated; and each phosphoprotein may exist as multiple phospho-isoforms that are present in low abundance and stoichiometry. Hence, phosphopeptide enrichment techniques are indispensable to (phospho)proteomics laboratories. These enrichment methods encompass widely-adopted techniques such as (i) affinity-based chromatography; (ii) ion exchange and mixed-mode chromatography (iii) enrichment with phospho-specific antibodies and protein domains, and (iv) functionalized polymers and other less common but emerging technologies such as hydroxyapatite chromatography and precipitation with inorganic ions. Here, we review these techniques, their history, continuous development and evaluation. Besides, we outline associating challenges of phosphoproteomics that are linked to experimental design, sample preparation, and proteolytic digestion. In addition, we also discuss about the future outlooks in phosphoproteomics, focusing on elucidating the noncanonical phosphoproteome and deciphering the "dark phosphoproteome". © 2020 John Wiley & Sons Ltd.
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Affiliation(s)
- Teck Yew Low
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, 56000, Kuala Lumpur, Malaysia
| | - M Aiman Mohtar
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, 56000, Kuala Lumpur, Malaysia
| | - Pey Yee Lee
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, 56000, Kuala Lumpur, Malaysia
| | - Nursyazwani Omar
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, 56000, Kuala Lumpur, Malaysia
| | - Houjiang Zhou
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, United Kingdom
| | - Mingliang Ye
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Centre, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
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Lone AM, Taskén K. Phosphoproteomics-Based Characterization of Prostaglandin E 2 Signaling in T Cells. Mol Pharmacol 2021; 99:370-382. [PMID: 33674363 DOI: 10.1124/molpharm.120.000170] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 03/01/2021] [Indexed: 12/24/2022] Open
Abstract
Prostaglandin E2 (PGE2) is a key lipid mediator in health and disease and serves as a crucial link between the immune response and cancer. With the advent of cancer therapies targeting PGE2 signaling pathways at different levels, there has been increased interest in mapping and understanding the complex and interconnected signaling pathways arising from the four distinct PGE2 receptors. Here, we review phosphoproteomics studies that have investigated different aspects of PGE2 signaling in T cells. These studies have elucidated PGE2's regulatory effect on T cell receptor signaling and T cell function, the key role of protein kinase A in many PGE2 signaling pathways, the temporal regulation of PGE2 signaling, differences in PGE2 signaling between different T cell subtypes, and finally, the crosstalk between PGE2 signaling pathways elicited by the four distinct PGE2 receptors present in T cells. SIGNIFICANCE STATEMENT: Through the reviewed studies, we now have a much better understanding of PGE2's signaling mechanisms and functional roles in T cells, as well as a solid platform for targeted and functional studies of specific PGE2-triggered pathways in T cells.
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Affiliation(s)
- Anna Mari Lone
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital (A.M.L., K.T.) and Institute for Clinical Medicine, University of Oslo, Oslo, Norway (K.T.)
| | - Kjetil Taskén
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital (A.M.L., K.T.) and Institute for Clinical Medicine, University of Oslo, Oslo, Norway (K.T.)
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Xu Y, Song X, Wang D, Wang Y, Li P, Li J. Proteomic insights into synaptic signaling in the brain: the past, present and future. Mol Brain 2021; 14:37. [PMID: 33596935 PMCID: PMC7888154 DOI: 10.1186/s13041-021-00750-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 02/09/2021] [Indexed: 12/29/2022] Open
Abstract
Chemical synapses in the brain connect neurons to form neural circuits, providing the structural and functional bases for neural communication. Disrupted synaptic signaling is closely related to a variety of neurological and psychiatric disorders. In the past two decades, proteomics has blossomed as a versatile tool in biological and biomedical research, rendering a wealth of information toward decoding the molecular machinery of life. There is enormous interest in employing proteomic approaches for the study of synapses, and substantial progress has been made. Here, we review the findings of proteomic studies of chemical synapses in the brain, with special attention paid to the key players in synaptic signaling, i.e., the synaptic protein complexes and their post-translational modifications. Looking toward the future, we discuss the technological advances in proteomics such as data-independent acquisition mass spectrometry (DIA-MS), cross-linking in combination with mass spectrometry (CXMS), and proximity proteomics, along with their potential to untangle the mystery of how the brain functions at the molecular level. Last but not least, we introduce the newly developed synaptomic methods. These methods and their successful applications marked the beginnings of the synaptomics era.
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Affiliation(s)
- Yalan Xu
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Medical College, Qingdao University, Qingdao, 266021, China
| | - Xiuyue Song
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Medical College, Qingdao University, Qingdao, 266021, China
| | - Dong Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Medical College, Qingdao University, Qingdao, 266021, China
| | - Yin Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Medical College, Qingdao University, Qingdao, 266021, China
| | - Peifeng Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Medical College, Qingdao University, Qingdao, 266021, China
| | - Jing Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Medical College, Qingdao University, Qingdao, 266021, China.
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Li J, Zhan X. Mass spectrometry-based proteomics analyses of post-translational modifications and proteoforms in human pituitary adenomas. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1869:140584. [PMID: 33321259 DOI: 10.1016/j.bbapap.2020.140584] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 12/06/2020] [Accepted: 12/08/2020] [Indexed: 12/13/2022]
Abstract
Pituitary adenoma (PA) is a common intracranial neoplasm, which affects the hypothalamus-pituitary-target organ axis systems, and is hazardous to human health. Post-translational modifications (PTMs), including phosphorylation, ubiquitination, nitration, and sumoylation, are vitally important in the PA pathogenesis. The large-scale analysis of PTMs could provide a global view of molecular mechanisms for PA. Proteoforms, which are used to define various protein structural and functional forms originated from the same gene, are the future direction of proteomics research. The global studies of different proteoforms and PTMs of hypophyseal hormones such as growth hormone (GH) and prolactin (PRL) and the proportion change of different GH proteoforms or PRL proteoforms in human pituitary tissue could provide new insights into the clinical value of pituitary hormones in PAs. Multiple quantitative proteomics methods, including mass spectrometry (MS)-based label-free and stable isotope-labeled strategies in combination with different PTM-peptide enrichment methods such as TiO2 enrichment of tryptic phosphopeptides and antibody enrichment of other PTM-peptides increase the feasibility for researchers to study PA proteomes. This article reviews the research status of PTMs and proteoforms in PAs, including the enrichment method, technical limitation, quantitative proteomics strategies, and the future perspectives, to achieve the goals of in-depth understanding its molecular pathogenesis, and discovering effective biomarkers and clinical therapeutic targets for predictive, preventive, and personalized treatment of PA patients.
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Affiliation(s)
- Jiajia Li
- University Creative Research Initiatives Center, Shandong First Medical University, 6699 Qingdao Road, Jinan, Shandong 250117, P. R. China; Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008 P. R. China; State Local Joint Engineering Laboratory for Anticancer Drugs, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008, PR China
| | - Xianquan Zhan
- University Creative Research Initiatives Center, Shandong First Medical University, 6699 Qingdao Road, Jinan, Shandong 250117, P. R. China; Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008 P. R. China; State Local Joint Engineering Laboratory for Anticancer Drugs, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008, PR China; Department of Oncology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008, PR China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008, PR China.
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13
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Smolikova G, Gorbach D, Lukasheva E, Mavropolo-Stolyarenko G, Bilova T, Soboleva A, Tsarev A, Romanovskaya E, Podolskaya E, Zhukov V, Tikhonovich I, Medvedev S, Hoehenwarter W, Frolov A. Bringing New Methods to the Seed Proteomics Platform: Challenges and Perspectives. Int J Mol Sci 2020; 21:E9162. [PMID: 33271881 PMCID: PMC7729594 DOI: 10.3390/ijms21239162] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 11/26/2020] [Accepted: 11/27/2020] [Indexed: 12/14/2022] Open
Abstract
For centuries, crop plants have represented the basis of the daily human diet. Among them, cereals and legumes, accumulating oils, proteins, and carbohydrates in their seeds, distinctly dominate modern agriculture, thus play an essential role in food industry and fuel production. Therefore, seeds of crop plants are intensively studied by food chemists, biologists, biochemists, and nutritional physiologists. Accordingly, seed development and germination as well as age- and stress-related alterations in seed vigor, longevity, nutritional value, and safety can be addressed by a broad panel of analytical, biochemical, and physiological methods. Currently, functional genomics is one of the most powerful tools, giving direct access to characteristic metabolic changes accompanying plant development, senescence, and response to biotic or abiotic stress. Among individual post-genomic methodological platforms, proteomics represents one of the most effective ones, giving access to cellular metabolism at the level of proteins. During the recent decades, multiple methodological advances were introduced in different branches of life science, although only some of them were established in seed proteomics so far. Therefore, here we discuss main methodological approaches already employed in seed proteomics, as well as those still waiting for implementation in this field of plant research, with a special emphasis on sample preparation, data acquisition, processing, and post-processing. Thereby, the overall goal of this review is to bring new methodologies emerging in different areas of proteomics research (clinical, food, ecological, microbial, and plant proteomics) to the broad society of seed biologists.
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Affiliation(s)
- Galina Smolikova
- Department of Plant Physiology and Biochemistry, St. Petersburg State University; 199034 St. Petersburg, Russia; (G.S.); (T.B.); (S.M.)
| | - Daria Gorbach
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
| | - Elena Lukasheva
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
| | - Gregory Mavropolo-Stolyarenko
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
| | - Tatiana Bilova
- Department of Plant Physiology and Biochemistry, St. Petersburg State University; 199034 St. Petersburg, Russia; (G.S.); (T.B.); (S.M.)
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry; 06120 Halle (Saale), Germany
| | - Alena Soboleva
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry; 06120 Halle (Saale), Germany
| | - Alexander Tsarev
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry; 06120 Halle (Saale), Germany
| | - Ekaterina Romanovskaya
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
| | - Ekaterina Podolskaya
- Institute of Analytical Instrumentation, Russian Academy of Science; 190103 St. Petersburg, Russia;
- Institute of Toxicology, Russian Federal Medical Agency; 192019 St. Petersburg, Russia
| | - Vladimir Zhukov
- All-Russia Research Institute for Agricultural Microbiology; 196608 St. Petersburg, Russia; (V.Z.); (I.T.)
| | - Igor Tikhonovich
- All-Russia Research Institute for Agricultural Microbiology; 196608 St. Petersburg, Russia; (V.Z.); (I.T.)
- Department of Genetics and Biotechnology, St. Petersburg State University; 199034 St. Petersburg, Russia
| | - Sergei Medvedev
- Department of Plant Physiology and Biochemistry, St. Petersburg State University; 199034 St. Petersburg, Russia; (G.S.); (T.B.); (S.M.)
| | - Wolfgang Hoehenwarter
- Proteome Analytics Research Group, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany;
| | - Andrej Frolov
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry; 06120 Halle (Saale), Germany
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14
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Hoopmann MR, Kusebauch U, Palmblad M, Bandeira N, Shteynberg DD, He L, Xia B, Stoychev SH, Omenn GS, Weintraub ST, Moritz RL. Insights from the First Phosphopeptide Challenge of the MS Resource Pillar of the HUPO Human Proteome Project. J Proteome Res 2020; 19:4754-4765. [PMID: 33166149 DOI: 10.1021/acs.jproteome.0c00648] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Mass spectrometry has greatly improved the analysis of phosphorylation events in complex biological systems and on a large scale. Despite considerable progress, the correct identification of phosphorylated sites, their quantification, and their interpretation regarding physiological relevance remain challenging. The MS Resource Pillar of the Human Proteome Organization (HUPO) Human Proteome Project (HPP) initiated the Phosphopeptide Challenge as a resource to help the community evaluate methods, learn procedures and data analysis routines, and establish their own workflows by comparing results obtained from a standard set of 94 phosphopeptides (serine, threonine, tyrosine) and their nonphosphorylated counterparts mixed at different ratios in a neat sample and a yeast background. Participants analyzed both samples with their method(s) of choice to report the identification and site localization of these peptides, determine their relative abundances, and enrich for the phosphorylated peptides in the yeast background. We discuss the results from 22 laboratories that used a range of different methods, instruments, and analysis software. We reanalyzed submitted data with a single software pipeline and highlight the successes and challenges in correct phosphosite localization. All of the data from this collaborative endeavor are shared as a resource to encourage the development of even better methods and tools for diverse phosphoproteomic applications. All submitted data and search results were uploaded to MassIVE (https://massive.ucsd.edu/) as data set MSV000085932 with ProteomeXchange identifier PXD020801.
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Affiliation(s)
| | - Ulrike Kusebauch
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Magnus Palmblad
- Center for Proteomics and Metabolomics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Nuno Bandeira
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California 92093, United States
| | | | - Lingjie He
- Synpeptide Co., Ltd., Shanghai 201204, China
| | - Bin Xia
- Synpeptide Co., Ltd., Shanghai 201204, China
| | | | - Gilbert S Omenn
- Institute for Systems Biology, Seattle, Washington 98109, United States.,Departments of Computational Medicine and Bioinformatics, Internal Medicine, and Human Genetics and School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Susan T Weintraub
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, United States
| | - Robert L Moritz
- Institute for Systems Biology, Seattle, Washington 98109, United States
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15
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Yang Y, Horvatovich P, Qiao L. Fragment Mass Spectrum Prediction Facilitates Site Localization of Phosphorylation. J Proteome Res 2020; 20:634-644. [PMID: 32985198 DOI: 10.1021/acs.jproteome.0c00580] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Liquid chromatography tandem mass spectrometry (LC-MS/MS) has been the most widely used technology for phosphoproteomics studies. As an alternative to database searching and probability-based phosphorylation site localization approaches, spectral library searching has been proved to be effective in the identification of phosphopeptides. However, incompletion of experimental spectral libraries limits the identification capability. Herein, we utilize MS/MS spectrum prediction coupled with spectral matching for site localization of phosphopeptides. In silico MS/MS spectra are generated from peptide sequences by deep learning/machine learning models trained with nonphosphopeptides. Then, mass shift according to phosphorylation sites, phosphoric acid neutral loss, and a "budding" strategy are adopted to adjust the in silico mass spectra. In silico MS/MS spectra can also be generated in one step for phosphopeptides using models trained with phosphopeptides. The method is benchmarked on data sets of synthetic phosphopeptides and is used to process real biological samples. It is demonstrated to be a method requiring only computational resources that supplements the probability-based approaches for phosphorylation site localization of singly and multiply phosphorylated peptides.
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Affiliation(s)
- Yi Yang
- Department of Chemistry and Shanghai Stomatological Hospital, Fudan University, Handan Road 220, Shanghai 200000, China
| | - Peter Horvatovich
- Department of Pharmacy, University of Groningen, Antonius Deusinglaan 1, Groningen 9700 AD, The Netherlands
| | - Liang Qiao
- Department of Chemistry and Shanghai Stomatological Hospital, Fudan University, Handan Road 220, Shanghai 200000, China
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16
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Igarashi M, Honda A, Kawasaki A, Nozumi M. Neuronal Signaling Involved in Neuronal Polarization and Growth: Lipid Rafts and Phosphorylation. Front Mol Neurosci 2020; 13:150. [PMID: 32922262 PMCID: PMC7456915 DOI: 10.3389/fnmol.2020.00150] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 07/16/2020] [Indexed: 12/17/2022] Open
Abstract
Neuronal polarization and growth are developmental processes that occur during neuronal cell differentiation. The molecular signaling mechanisms involved in these events in in vivo mammalian brain remain unclear. Also, cellular events of the neuronal polarization process within a given neuron are thought to be constituted of many independent intracellular signal transduction pathways (the "tug-of-war" model). However, in vivo results suggest that such pathways should be cooperative with one another among a given group of neurons in a region of the brain. Lipid rafts, specific membrane domains with low fluidity, are candidates for the hotspots of such intracellular signaling. Among the signals reported to be involved in polarization, a number are thought to be present or translocated to the lipid rafts in response to extracellular signals. As part of our analysis, we discuss how such novel molecular mechanisms are combined for effective regulation of neuronal polarization and growth, focusing on the significance of the lipid rafts, including results based on recently introduced methods.
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Affiliation(s)
- Michihiro Igarashi
- Department of Neurochemistry and Molecular Cell Biology, Niigata University School of Medicine and Graduate School of Medical/Dental Sciences, Niigata, Japan
| | - Atsuko Honda
- Department of Neurochemistry and Molecular Cell Biology, Niigata University School of Medicine and Graduate School of Medical/Dental Sciences, Niigata, Japan
| | - Asami Kawasaki
- Department of Neurochemistry and Molecular Cell Biology, Niigata University School of Medicine and Graduate School of Medical/Dental Sciences, Niigata, Japan
| | - Motohiro Nozumi
- Department of Neurochemistry and Molecular Cell Biology, Niigata University School of Medicine and Graduate School of Medical/Dental Sciences, Niigata, Japan
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17
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Thingholm TE, Rönnstrand L, Rosenberg PA. Why and how to investigate the role of protein phosphorylation in ZIP and ZnT zinc transporter activity and regulation. Cell Mol Life Sci 2020; 77:3085-3102. [PMID: 32076742 PMCID: PMC7391401 DOI: 10.1007/s00018-020-03473-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 01/13/2020] [Accepted: 01/28/2020] [Indexed: 12/20/2022]
Abstract
Zinc is required for the regulation of proliferation, metabolism, and cell signaling. It is an intracellular second messenger, and the cellular level of ionic, mobile zinc is strictly controlled by zinc transporters. In mammals, zinc homeostasis is primarily regulated by ZIP and ZnT zinc transporters. The importance of these transporters is underscored by the list of diseases resulting from changes in transporter expression and activity. However, despite numerous structural studies of the transporters revealing both zinc binding sites and motifs important for transporter function, the exact molecular mechanisms regulating ZIP and ZnT activities are still not clear. For example, protein phosphorylation was found to regulate ZIP7 activity resulting in the release of Zn2+ from intracellular stores leading to phosphorylation of tyrosine kinases and activation of signaling pathways. In addition, sequence analyses predict all 24 human zinc transporters to be phosphorylated suggesting that protein phosphorylation is important for regulation of transporter function. This review describes how zinc transporters are implicated in a number of important human diseases. It summarizes the current knowledge regarding ZIP and ZnT transporter structures and points to how protein phosphorylation seems to be important for the regulation of zinc transporter activity. The review addresses the need to investigate the role of protein phosphorylation in zinc transporter function and regulation, and argues for a pressing need to introduce quantitative phosphoproteomics to specifically target zinc transporters and proteins involved in zinc signaling. Finally, different quantitative phosphoproteomic strategies are suggested.
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Affiliation(s)
- T E Thingholm
- Department of Molecular Medicine, Cancer and Inflammation Research, University of Southern Denmark, J.B. Winsløws Vej 25, 3, 5000, Odense C, Denmark.
| | - L Rönnstrand
- Division of Translational Cancer Research, Lund University, Medicon Village, Building 404, Scheelevägen 2, Lund, Sweden
- Lund Stem Cell Center, Lund University, Medicon Village, Building 404, Scheelevägen 2, Lund, Sweden
- Division of Oncology, Skåne University Hospital, Lund, Sweden
| | - P A Rosenberg
- Department of Neurology and F.M. Kirby Neurobiology Center, Boston Children's Hospital, 300 Longwood Ave, Boston, MA, 02115, USA
- Department of Neurology and Program in Neuroscience, Harvard Medical School, Boston, MA, 02115, USA
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18
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Investigation of cancer drug resistance mechanisms by phosphoproteomics. Pharmacol Res 2020; 160:105091. [PMID: 32712320 DOI: 10.1016/j.phrs.2020.105091] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 07/20/2020] [Accepted: 07/20/2020] [Indexed: 12/23/2022]
Abstract
Cancer cell mutations can be identified by genomic and transcriptomic techniques. However, they are not sufficient to understand the full complexity of cancer heterogeneity. Analyses of proteins expressed in cancers and their modification profiles show how these mutations could be translated at the functional level. Protein phosphorylation is a major post-translational modification critical for regulating several cellular functions. The covalent addition of phosphate groups to serine, threonine, and tyrosine is catalyzed by protein kinases. Over the past years, kinases were strongly associated with cancer, thus inhibition of protein kinases emanated as novel cancer treatment. However, cancers frequently develop drug resistance. Therefore, a better understanding of drug effects on tumors is urgently needed. In this perspective, phosphoproteomics arose as advanced tool to monitor cancer therapies and to discover novel drugs. This review highlights the role of phosphoproteomics in predicting sensitivity or resistance of cancers towards tyrosine kinase inhibitors and cytotoxic drugs. It also shows the importance of phosphoproteomics in identifying biomarkers that could be applied in clinical diagnostics to predict responses to drugs.
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19
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Scheidt T, Alka O, Gonczarowska-Jorge H, Gruber W, Rathje F, Dell’Aica M, Rurik M, Kohlbacher O, Zahedi RP, Aberger F, Huber CG. Phosphoproteomics of short-term hedgehog signaling in human medulloblastoma cells. Cell Commun Signal 2020; 18:99. [PMID: 32576205 PMCID: PMC7310537 DOI: 10.1186/s12964-020-00591-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Accepted: 05/05/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Aberrant hedgehog (HH) signaling is implicated in the development of various cancer entities such as medulloblastoma. Activation of GLI transcription factors was revealed as the driving force upon pathway activation. Increased phosphorylation of essential effectors such as Smoothened (SMO) and GLI proteins by kinases including Protein Kinase A, Casein Kinase 1, and Glycogen Synthase Kinase 3 β controls effector activity, stability and processing. However, a deeper and more comprehensive understanding of phosphorylation in the signal transduction remains unclear, particularly during early response processes involved in SMO activation and preceding GLI target gene regulation. METHODS We applied temporal quantitative phosphoproteomics to reveal phosphorylation dynamics underlying the short-term chemical activation and inhibition of early hedgehog signaling in HH responsive human medulloblastoma cells. Medulloblastoma cells were treated for 5.0 and 15 min with Smoothened Agonist (SAG) to induce and with vismodegib to inhibit the HH pathway. RESULTS Our phosphoproteomic profiling resulted in the quantification of 7700 and 10,000 phosphosites after 5.0 and 15 min treatment, respectively. The data suggest a central role of phosphorylation in the regulation of ciliary assembly, trafficking, and signal transduction already after 5.0 min treatment. ERK/MAPK signaling, besides Protein Kinase A signaling and mTOR signaling, were differentially regulated after short-term treatment. Activation of Polo-like Kinase 1 and inhibition of Casein Kinase 2A1 were characteristic for vismodegib treatment, while SAG treatment induced Aurora Kinase A activity. Distinctive phosphorylation of central players of HH signaling such as SMO, SUFU, GLI2 and GLI3 was observed only after 15 min treatment. CONCLUSIONS This study provides evidence that phosphorylation triggered in response to SMO modulation dictates the localization of hedgehog pathway components within the primary cilium and affects the regulation of the SMO-SUFU-GLI axis. The data are relevant for the development of targeted therapies of HH-associated cancers including sonic HH-type medulloblastoma. A deeper understanding of the mechanisms of action of SMO inhibitors such as vismodegib may lead to the development of compounds causing fewer adverse effects and lower frequencies of drug resistance. Video Abstract.
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Affiliation(s)
- Tamara Scheidt
- Department of Biosciences, Bioanalytical Research Laboratories and Molecular Cancer Research and Tumor Immunology, Cancer Cluster Salzburg, University of Salzburg, Hellbrunner Straße 34, 5020 Salzburg, Austria
| | - Oliver Alka
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Sand 14, 72076 Tübingen, Germany
| | - Humberto Gonczarowska-Jorge
- Leibniz-Institute of Analytical Sciences- ISAS - e.V, Dortmund, Germany
- Present address: CAPES Foundation, Ministry of Education of Brazil, Brasília, DF 70040-020 Brazil
| | - Wolfgang Gruber
- Department of Biosciences, Bioanalytical Research Laboratories and Molecular Cancer Research and Tumor Immunology, Cancer Cluster Salzburg, University of Salzburg, Hellbrunner Straße 34, 5020 Salzburg, Austria
- Present address: EVER Valinject GmbH, 4866 Unterach am Attersee, Austria
| | - Florian Rathje
- Department of Biosciences, Bioanalytical Research Laboratories and Molecular Cancer Research and Tumor Immunology, Cancer Cluster Salzburg, University of Salzburg, Hellbrunner Straße 34, 5020 Salzburg, Austria
| | | | - Marc Rurik
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Sand 14, 72076 Tübingen, Germany
| | - Oliver Kohlbacher
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Sand 14, 72076 Tübingen, Germany
- Biomolecular Interactions, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany
- Institute for Translational Bioinformatics, University Hospital Tübingen, Hoppe-Seyler-Str. 9, 72076 Tübingen, Germany
- Applied Bioinformatics, Center for Bioinformatics, University of Tübingen, Sand 14, 72076 Tübingen, Germany
| | - René P. Zahedi
- Leibniz-Institute of Analytical Sciences- ISAS - e.V, Dortmund, Germany
- Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, Montreal, Canada
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Canada
| | - Fritz Aberger
- Department of Biosciences, Bioanalytical Research Laboratories and Molecular Cancer Research and Tumor Immunology, Cancer Cluster Salzburg, University of Salzburg, Hellbrunner Straße 34, 5020 Salzburg, Austria
| | - Christian G. Huber
- Department of Biosciences, Bioanalytical Research Laboratories and Molecular Cancer Research and Tumor Immunology, Cancer Cluster Salzburg, University of Salzburg, Hellbrunner Straße 34, 5020 Salzburg, Austria
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20
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Dengjel J, Bruckner-Tuderman L, Nyström A. Skin proteomics - analysis of the extracellular matrix in health and disease. Expert Rev Proteomics 2020; 17:377-391. [PMID: 32552150 DOI: 10.1080/14789450.2020.1773261] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
INTRODUCTION The skin protects the human body from external insults and regulates water and temperature homeostasis. A highly developed extracellular matrix (ECM) supports the skin and instructs its cell functions. Reduced functionality of the ECM is often associated with skin diseases that cause physical impairment and also have implications on social interactions and quality of life of affected individuals. AREAS COVERED With a focus on the skin ECM we discuss how mass spectrometry (MS)-based proteomic approaches first contributed to establishing skin protein inventories and then facilitated elucidation of molecular functions and disease mechanisms. EXPERT OPINION MS-based proteomic approaches have significantly contributed to our understanding of skin pathophysiology, but also revealed the challenges in assessing the skin ECM. The numerous posttranslational modifications of ECM proteins, like glycosylation, crosslinking, oxidation, and proteolytic maturation in disease settings can be difficult to tackle and remain understudied. Increased ease of handling of LC-MS/MS systems and automated/streamlined data analysis pipelines together with the accompanying increased usage of LC-MS/MS approaches will ensure that in the coming years MS-based proteomic approaches will continue to play a vital part in skin disease research. They will facilitate the elucidation of molecular disease mechanisms and, ultimately, identification of new druggable targets.
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Affiliation(s)
- Jörn Dengjel
- Department of Biology, University of Fribourg , Fribourg, Switzerland
| | - Leena Bruckner-Tuderman
- Department of Dermatology, Faculty of Medicine, Medical Center - University of Freiburg , Freiburg, University of Freiburg, Freiburg, Germany Germany
| | - Alexander Nyström
- Department of Dermatology, Faculty of Medicine, Medical Center - University of Freiburg , Freiburg, University of Freiburg, Freiburg, Germany Germany
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21
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Bensimon A, Koch JP, Francica P, Roth SM, Riedo R, Glück AA, Orlando E, Blaukat A, Aebersold DM, Zimmer Y, Aebersold R, Medová M. Deciphering MET-dependent modulation of global cellular responses to DNA damage by quantitative phosphoproteomics. Mol Oncol 2020; 14:1185-1206. [PMID: 32336009 PMCID: PMC7266272 DOI: 10.1002/1878-0261.12696] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 03/18/2020] [Accepted: 04/22/2020] [Indexed: 12/17/2022] Open
Abstract
Increasing evidence suggests that interference with growth factor receptor tyrosine kinase (RTK) signaling can affect DNA damage response (DDR) networks, with a consequent impact on cellular responses to DNA‐damaging agents widely used in cancer treatment. In that respect, the MET RTK is deregulated in abundance and/or activity in a variety of human tumors. Using two proteomic techniques, we explored how disrupting MET signaling modulates global cellular phosphorylation response to ionizing radiation (IR). Following an immunoaffinity‐based phosphoproteomic discovery survey, we selected candidate phosphorylation sites for extensive characterization by targeted proteomics focusing on phosphorylation sites in both signaling networks. Several substrates of the DDR were confirmed to be modulated by sequential MET inhibition and IR, or MET inhibition alone. Upon combined treatment, for two substrates, NUMA1 S395 and CHEK1 S345, the gain and loss of phosphorylation, respectively, were recapitulated using invivo tumor models by immunohistochemistry, with possible utility in future translational research. Overall, we have corroborated phosphorylation sites at the intersection between MET and the DDR signaling networks, and suggest that these represent a class of proteins at the interface between oncogene‐driven proliferation and genomic stability.
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Affiliation(s)
- Ariel Bensimon
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Switzerland
| | - Jonas P Koch
- Department of Radiation Oncology, Inselspital, Bern University Hospital, University of Bern, Switzerland.,Department for BioMedical Research, Inselspital, Bern University Hospital, University of Bern, Switzerland
| | - Paola Francica
- Department of Radiation Oncology, Inselspital, Bern University Hospital, University of Bern, Switzerland.,Department for BioMedical Research, Inselspital, Bern University Hospital, University of Bern, Switzerland
| | - Selina M Roth
- Department of Radiation Oncology, Inselspital, Bern University Hospital, University of Bern, Switzerland.,Department for BioMedical Research, Inselspital, Bern University Hospital, University of Bern, Switzerland
| | - Rahel Riedo
- Department of Radiation Oncology, Inselspital, Bern University Hospital, University of Bern, Switzerland.,Department for BioMedical Research, Inselspital, Bern University Hospital, University of Bern, Switzerland
| | - Astrid A Glück
- Department of Radiation Oncology, Inselspital, Bern University Hospital, University of Bern, Switzerland.,Department for BioMedical Research, Inselspital, Bern University Hospital, University of Bern, Switzerland
| | - Eleonora Orlando
- Department of Radiation Oncology, Inselspital, Bern University Hospital, University of Bern, Switzerland.,Department for BioMedical Research, Inselspital, Bern University Hospital, University of Bern, Switzerland
| | - Andree Blaukat
- Global Research & Development, Merck KGaA, Darmstadt, Germany
| | - Daniel M Aebersold
- Department of Radiation Oncology, Inselspital, Bern University Hospital, University of Bern, Switzerland.,Department for BioMedical Research, Inselspital, Bern University Hospital, University of Bern, Switzerland
| | - Yitzhak Zimmer
- Department of Radiation Oncology, Inselspital, Bern University Hospital, University of Bern, Switzerland.,Department for BioMedical Research, Inselspital, Bern University Hospital, University of Bern, Switzerland
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Switzerland.,Faculty of Science, University of Zürich, Switzerland
| | - Michaela Medová
- Department of Radiation Oncology, Inselspital, Bern University Hospital, University of Bern, Switzerland.,Department for BioMedical Research, Inselspital, Bern University Hospital, University of Bern, Switzerland
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22
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Watson NA, Cartwright TN, Lawless C, Cámara-Donoso M, Sen O, Sako K, Hirota T, Kimura H, Higgins JMG. Kinase inhibition profiles as a tool to identify kinases for specific phosphorylation sites. Nat Commun 2020; 11:1684. [PMID: 32245944 PMCID: PMC7125195 DOI: 10.1038/s41467-020-15428-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 03/06/2020] [Indexed: 01/08/2023] Open
Abstract
There are thousands of known cellular phosphorylation sites, but the paucity of ways to identify kinases for particular phosphorylation events remains a major roadblock for understanding kinase signaling. To address this, we here develop a generally applicable method that exploits the large number of kinase inhibitors that have been profiled on near-kinome-wide panels of protein kinases. The inhibition profile for each kinase provides a fingerprint that allows identification of unknown kinases acting on target phosphosites in cell extracts. We validate the method on diverse known kinase-phosphosite pairs, including histone kinases, EGFR autophosphorylation, and Integrin β1 phosphorylation by Src-family kinases. We also use our approach to identify the previously unknown kinases responsible for phosphorylation of INCENP at a site within a commonly phosphorylated motif in mitosis (a non-canonical target of Cyclin B-Cdk1), and of BCL9L at S915 (PKA). We show that the method has clear advantages over in silico and genetic screening.
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Affiliation(s)
- Nikolaus A Watson
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Tyrell N Cartwright
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Conor Lawless
- Wellcome Centre for Mitochondrial Research, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Marcos Cámara-Donoso
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Onur Sen
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Kosuke Sako
- The Cancer Institute, Japanese Foundation for Cancer Research, Koto, Tokyo, 135-8550, Japan
| | - Toru Hirota
- The Cancer Institute, Japanese Foundation for Cancer Research, Koto, Tokyo, 135-8550, Japan
| | - Hiroshi Kimura
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Kanagawa, 226-8503, Japan
| | - Jonathan M G Higgins
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.
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Chua XY, Mensah T, Aballo T, Mackintosh SG, Edmondson RD, Salomon AR. Tandem Mass Tag Approach Utilizing Pervanadate BOOST Channels Delivers Deeper Quantitative Characterization of the Tyrosine Phosphoproteome. Mol Cell Proteomics 2020; 19:730-743. [PMID: 32071147 PMCID: PMC7124467 DOI: 10.1074/mcp.tir119.001865] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 02/07/2020] [Indexed: 01/08/2023] Open
Abstract
Dynamic tyrosine phosphorylation is fundamental to a myriad of cellular processes. However, the inherently low abundance of tyrosine phosphorylation in the proteome and the inefficient enrichment of phosphotyrosine(pTyr)-containing peptides has led to poor pTyr peptide identification and quantitation, critically hindering researchers' ability to elucidate signaling pathways regulated by tyrosine phosphorylation in systems where cellular material is limited. The most popular approaches to wide-scale characterization of the tyrosine phosphoproteome use pTyr enrichment with pan-specific, anti-pTyr antibodies from a large amount of starting material. Methods that decrease the amount of starting material and increase the characterization depth of the tyrosine phosphoproteome while maintaining quantitative accuracy and precision would enable the discovery of tyrosine phosphorylation networks in rarer cell populations. To achieve these goals, the BOOST (Broad-spectrum Optimization Of Selective Triggering) method leveraging the multiplexing capability of tandem mass tags (TMT) and the use of pervanadate (PV) boost channels (cells treated with the broad-spectrum tyrosine phosphatase inhibitor PV) selectively increased the relative abundance of pTyr-containing peptides. After PV boost channels facilitated selective fragmentation of pTyr-containing peptides, TMT reporter ions delivered accurate quantitation of each peptide for the experimental samples while the quantitation from PV boost channels was ignored. This method yielded up to 6.3-fold boost in pTyr quantification depth of statistically significant data derived from contrived ratios, compared with TMT without PV boost channels or intensity-based label-free (LF) quantitation while maintaining quantitative accuracy and precision, allowing quantitation of over 2300 unique pTyr peptides from only 1 mg of T cell receptor-stimulated Jurkat T cells. The BOOST strategy can potentially be applied in analyses of other post-translational modifications where treatments that broadly elevate the levels of those modifications across the proteome are available.
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Affiliation(s)
- Xien Yu Chua
- Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, Rhode Island
| | - Theresa Mensah
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island
| | - Timothy Aballo
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island
| | - Samuel G Mackintosh
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Ricky D Edmondson
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Arthur R Salomon
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island.
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Prospects and challenges of multi-omics data integration in toxicology. Arch Toxicol 2020; 94:371-388. [PMID: 32034435 DOI: 10.1007/s00204-020-02656-y] [Citation(s) in RCA: 111] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 01/29/2020] [Indexed: 12/13/2022]
Abstract
Exposure of cells or organisms to chemicals can trigger a series of effects at the regulatory pathway level, which involve changes of levels, interactions, and feedback loops of biomolecules of different types. A single-omics technique, e.g., transcriptomics, will detect biomolecules of one type and thus can only capture changes in a small subset of the biological cascade. Therefore, although applying single-omics analyses can lead to the identification of biomarkers for certain exposures, they cannot provide a systemic understanding of toxicity pathways or adverse outcome pathways. Integration of multiple omics data sets promises a substantial improvement in detecting this pathway response to a toxicant, by an increase of information as such and especially by a systemic understanding. Here, we report the findings of a thorough evaluation of the prospects and challenges of multi-omics data integration in toxicological research. We review the availability of such data, discuss options for experimental design, evaluate methods for integration and analysis of multi-omics data, discuss best practices, and identify knowledge gaps. Re-analyzing published data, we demonstrate that multi-omics data integration can considerably improve the confidence in detecting a pathway response. Finally, we argue that more data need to be generated from studies with a multi-omics-focused design, to define which omics layers contribute most to the identification of a pathway response to a toxicant.
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25
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Parsons J, Francavilla C. 'Omics Approaches to Explore the Breast Cancer Landscape. Front Cell Dev Biol 2020; 7:395. [PMID: 32039208 PMCID: PMC6987401 DOI: 10.3389/fcell.2019.00395] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 12/30/2019] [Indexed: 12/24/2022] Open
Abstract
Breast cancer incidence is increasing worldwide with more than 600,000 deaths reported in 2018 alone. In current practice treatment options for breast cancer patients consists of surgery, chemotherapy, radiotherapy or targeting of classical markers of breast cancer subtype: estrogen receptor (ER) and HER2. However, these treatments fail to prevent recurrence and metastasis. Improved understanding of breast cancer and metastasis biology will help uncover novel biomarkers and therapeutic opportunities to improve patient stratification and treatment. We will first provide an overview of current methods and models used to study breast cancer biology, focusing on 2D and 3D cell culture, including organoids, and on in vivo models such as the MMTV mouse model and patient-derived xenografts (PDX). Next, genomic, transcriptomic, and proteomic approaches and their integration will be considered in the context of breast cancer susceptibility, breast cancer drivers, and therapeutic response and resistance to treatment. Finally, we will discuss how 'Omics datasets in combination with traditional breast cancer models are useful for generating insights into breast cancer biology, for suggesting individual treatments in precision oncology, and for creating data repositories to undergo further meta-analysis. System biology has the potential to catalyze the next great leap forward in treatment options for breast cancer patients.
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Affiliation(s)
- Joseph Parsons
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester, United Kingdom
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Chiara Francavilla
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester, United Kingdom
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Deb B, George IA, Sharma J, Kumar P. Phosphoproteomics Profiling to Identify Altered Signaling Pathways and Kinase-Targeted Cancer Therapies. Methods Mol Biol 2020; 2051:241-264. [PMID: 31552632 DOI: 10.1007/978-1-4939-9744-2_10] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Phosphorylation is one of the most extensively studied posttranslational modifications (PTM), which regulates cellular functions like cell growth, differentiation, apoptosis, and cell signaling. Kinase families cover a wide number of oncoproteins and are strongly associated with cancer. Identification of driver kinases is an intense area of cancer research. Thus, kinases serve as the potential target to improve the efficacy of targeted therapies. Mass spectrometry-based phosphoproteomic approach has paved the way to the identification of a large number of altered phosphorylation events in proteins and signaling cascades that may lead to oncogenic processes in a cell. Alterations in signaling pathways result in the activation of oncogenic processes predominantly regulated by kinases and phosphatases. Therefore, drugs such as kinase inhibitors, which target dysregulated pathways, represent a promising area for cancer therapy.
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Affiliation(s)
- Barnali Deb
- Institute of Bioinformatics, International Technology Park, Bangalore, India.,Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
| | - Irene A George
- Institute of Bioinformatics, International Technology Park, Bangalore, India
| | - Jyoti Sharma
- Institute of Bioinformatics, International Technology Park, Bangalore, India.,Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
| | - Prashant Kumar
- Institute of Bioinformatics, International Technology Park, Bangalore, India. .,Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India.
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27
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Optimization of TripleTOF spectral simulation and library searching for confident localization of phosphorylation sites. PLoS One 2019; 14:e0225885. [PMID: 31790495 PMCID: PMC6886777 DOI: 10.1371/journal.pone.0225885] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Accepted: 11/14/2019] [Indexed: 12/31/2022] Open
Abstract
Tandem mass spectrometry (MS/MS) has been used in analysis of proteins and their post-translational modifications. A recently developed data analysis method, which simulates MS/MS spectra of phosphopeptides and performs spectral library searching using SpectraST, facilitates confident localization of phosphorylation sites. However, its performance has been evaluated only on MS/MS spectra acquired using Orbitrap HCD mass spectrometers so far. In this study, we have investigated whether this approach would be applicable to another type of mass spectrometers, and optimized the simulation and search conditions to achieve sensitive and confident site localization. Synthetic phosphopeptides and enriched K562 cell phosphopeptides were analyzed using a TripleTOF 6600 mass spectrometer before and after enzymatic dephosphorylation. Dephosphorylated peptides identified by X!Tandem database searching were subjected to spectral simulation of all possible single phosphorylations using SimPhospho software. Phosphopeptides were identified and localized by SpectraST searching against a library of the simulated spectra. Although no synthetic phosphopeptide was localized at 1% false localization rate under the previous conditions, optimization of the spectral simulation and search conditions for the TripleTOF datasets achieved the localization and improved the sensitivity. Furthermore, the optimized conditions enabled sensitive localization of K562 phosphopeptides at 1% false discovery and localization rates. These results suggest that accurate phosphopeptide simulation of TripleTOF MS/MS spectra is possible and the simulated spectral libraries can be used in SpectraST searching for confident localization of phosphorylation sites.
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Abstract
Castration-resistant prostate cancer (CRPC) remains incurable despite the approval of several new treatments. Identification of new biomarkers and therapeutic targets to enable personalization of CRPC therapy, with the aim of maximizing therapeutic responses and minimizing toxicity in patients, is urgently needed. Prostate cancer progression and therapeutic resistance are frequently driven by aberrantly activated kinase signalling pathways that are amenable to pharmacological inhibition. Personalized phosphoproteomics, which enables the analysis of signalling networks in individual tumours, is a promising approach to advance personalized therapy by discovering biomarkers of pathway activity and clinically actionable targets. Several technologies for global and targeted phosphoproteomic analysis exist, each with its own strengths and shortcomings. Global discovery phosphoproteomics is predominantly conducted using liquid chromatography-tandem mass spectrometry coupled with data-dependent or data-independent acquisition technologies. Multiplexed targeted phosphoproteomics can be divided into platforms based on mass spectrometry or antibodies, including selected or parallel reaction monitoring and triggered by offset, multiplexed, accurate mass, high-resolution, absolute quantification (known as TOMAHAQ) or forward-phase or reverse-phase protein arrays, respectively. Several obstacles still need to be overcome before the full potential of phosphoproteomics can be realized in routine clinical practice, but a future phosphoproteomics-centric trans-omic profiling approach should enable optimized personalized CRPC management through improved biomarkers and targeted treatments.
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29
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Mnatsakanyan R, Shema G, Basik M, Batist G, Borchers CH, Sickmann A, Zahedi RP. Detecting post-translational modification signatures as potential biomarkers in clinical mass spectrometry. Expert Rev Proteomics 2019; 15:515-535. [PMID: 29893147 DOI: 10.1080/14789450.2018.1483340] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
INTRODUCTION Numerous diseases are caused by changes in post-translational modifications (PTMs). Therefore, the number of clinical proteomics studies that include the analysis of PTMs is increasing. Combining complementary information-for example changes in protein abundance, PTM levels, with the genome and transcriptome (proteogenomics)-holds great promise for discovering important drivers and markers of disease, as variations in copy number, expression levels, or mutations without spatial/functional/isoform information is often insufficient or even misleading. Areas covered: We discuss general considerations, requirements, pitfalls, and future perspectives in applying PTM-centric proteomics to clinical samples. This includes samples obtained from a human subject, for instance (i) bodily fluids such as plasma, urine, or cerebrospinal fluid, (ii) primary cells such as reproductive cells, blood cells, and (iii) tissue samples/biopsies. Expert commentary: PTM-centric discovery proteomics can substantially contribute to the understanding of disease mechanisms by identifying signatures with potential diagnostic or even therapeutic relevance but may require coordinated efforts of interdisciplinary and eventually multi-national consortia, such as initiated in the cancer moonshot program. Additionally, robust and standardized mass spectrometry (MS) assays-particularly targeted MS, MALDI imaging, and immuno-MALDI-may be transferred to the clinic to improve patient stratification for precision medicine, and guide therapies.
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Affiliation(s)
- Ruzanna Mnatsakanyan
- a Protein Dynamics , Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V , Dortmund , 44227 , Germany
| | - Gerta Shema
- a Protein Dynamics , Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V , Dortmund , 44227 , Germany
| | - Mark Basik
- b Gerald Bronfman Department of Oncology , Jewish General Hospital, McGill University , Montreal , Quebec H4A 3T2 , Canada
| | - Gerald Batist
- b Gerald Bronfman Department of Oncology , Jewish General Hospital, McGill University , Montreal , Quebec H4A 3T2 , Canada
| | - Christoph H Borchers
- b Gerald Bronfman Department of Oncology , Jewish General Hospital, McGill University , Montreal , Quebec H4A 3T2 , Canada.,c University of Victoria-Genome British Columbia Proteomics Centre, University of Victoria , Victoria , British Columbia V8Z 7X8 , Canada.,d Department of Biochemistry and Microbiology , University of Victoria , Victoria , British Columbia , V8P 5C2 , Canada.,e Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University , Montreal , Quebec H3T 1E2 , Canada
| | - Albert Sickmann
- a Protein Dynamics , Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V , Dortmund , 44227 , Germany.,f Medizinische Fakultät, Medizinische Proteom-Center (MPC), Ruhr-Universität Bochum , 44801 Bochum , Germany.,g Department of Chemistry , College of Physical Sciences, University of Aberdeen , Aberdeen AB24 3FX , Scotland , United Kingdom
| | - René P Zahedi
- a Protein Dynamics , Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V , Dortmund , 44227 , Germany.,b Gerald Bronfman Department of Oncology , Jewish General Hospital, McGill University , Montreal , Quebec H4A 3T2 , Canada.,e Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University , Montreal , Quebec H3T 1E2 , Canada
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IGARASHI M. Molecular basis of the functions of the mammalian neuronal growth cone revealed using new methods. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2019; 95:358-377. [PMID: 31406059 PMCID: PMC6766448 DOI: 10.2183/pjab.95.026] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 04/26/2019] [Indexed: 05/25/2023]
Abstract
The neuronal growth cone is a highly motile, specialized structure for extending neuronal processes. This structure is essential for nerve growth, axon pathfinding, and accurate synaptogenesis. Growth cones are important not only during development but also for plasticity-dependent synaptogenesis and neuronal circuit rearrangement following neural injury in the mature brain. However, the molecular details of mammalian growth cone function are poorly understood. This review examines molecular findings on the function of the growth cone as a result of the introduction of novel methods such superresolution microscopy and (phospho)proteomics. These results increase the scope of our understating of the molecular mechanisms of growth cone behavior in the mammalian brain.
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Affiliation(s)
- Michihiro IGARASHI
- Department of Neurochemistry and Molecular Cell Biology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
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31
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Pandeswari PB, Sabareesh V. Middle-down approach: a choice to sequence and characterize proteins/proteomes by mass spectrometry. RSC Adv 2018; 9:313-344. [PMID: 35521579 PMCID: PMC9059502 DOI: 10.1039/c8ra07200k] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 12/11/2018] [Indexed: 12/27/2022] Open
Abstract
Owing to rapid growth in the elucidation of genome sequences of various organisms, deducing proteome sequences has become imperative, in order to have an improved understanding of biological processes. Since the traditional Edman method was unsuitable for high-throughput sequencing and also for N-terminus modified proteins, mass spectrometry (MS) based methods, mainly based on soft ionization modes: electrospray ionization and matrix-assisted laser desorption/ionization, began to gain significance. MS based methods were adaptable for high-throughput studies and applicable for sequencing N-terminus blocked proteins/peptides too. Consequently, over the last decade a new discipline called 'proteomics' has emerged, which encompasses the attributes necessary for high-throughput identification of proteins. 'Proteomics' may also be regarded as an offshoot of the classic field, 'biochemistry'. Many protein sequencing and proteomic investigations were successfully accomplished through MS dependent sequence elucidation of 'short proteolytic peptides (typically: 7-20 amino acid residues), which is called the 'shotgun' or 'bottom-up (BU)' approach. While the BU approach continues as a workhorse for proteomics/protein sequencing, attempts to sequence intact proteins without proteolysis, called the 'top-down (TD)' approach started, due to ambiguities in the BU approach, e.g., protein inference problem, identification of proteoforms and the discovery of posttranslational modifications (PTMs). The high-throughput TD approach (TD proteomics) is yet in its infancy. Nevertheless, TD characterization of purified intact proteins has been useful for detecting PTMs. With the hope to overcome the pitfalls of BU and TD strategies, another concept called the 'middle-down (MD)' approach was put forward. Similar to BU, the MD approach also involves proteolysis, but in a restricted manner, to produce 'longer' proteolytic peptides than the ones usually obtained in BU studies, thereby providing better sequence coverage. In this regard, special proteases (OmpT, Sap9, IdeS) have been used, which can cleave proteins to produce longer proteolytic peptides. By reviewing ample evidences currently existing in the literature that is predominantly on PTM characterization of histones and antibodies, herein we highlight salient features of the MD approach. Consequently, we are inclined to claim that the MD concept might have widespread applications in future for various research areas, such as clinical, biopharmaceuticals (including PTM analysis) and even for general/routine characterization of proteins including therapeutic proteins, but not just limited to analysis of histones or antibodies.
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Affiliation(s)
- P Boomathi Pandeswari
- Advanced Centre for Bio Separation Technology (CBST), Vellore Institute of Technology (VIT) Vellore Tamil Nadu 632014 India
| | - Varatharajan Sabareesh
- Advanced Centre for Bio Separation Technology (CBST), Vellore Institute of Technology (VIT) Vellore Tamil Nadu 632014 India
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32
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Wang L, Li S, Tang H. msCRUSH: Fast Tandem Mass Spectral Clustering Using Locality Sensitive Hashing. J Proteome Res 2018; 18:147-158. [PMID: 30511858 DOI: 10.1021/acs.jproteome.8b00448] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Large-scale proteomics projects often generate massive and highly redundant tandem mass spectra. Spectral clustering algorithms can reduce the redundancy in these data sets and thus speed up database searching for peptide identification, a major bottleneck for proteomic data analysis. The key challenge of spectral clustering is to reduce the redundancy in the MS/MS spectra data while retaining sufficient sensitivity to identify peptides from the clustered spectra. We present the software msCRUSH, which implements a novel spectral clustering algorithm based on the locality sensitive hashing technique. When tested on a large-scale proteomic data set consisting of 23.6 million spectra (including 14.4 million spectra of charge 2+), msCRUSH runs 6.9-11.3 times faster than the state-of-the-art spectral clustering software, PRIDE Cluster, while achieving higher clustering sensitivity and comparable accuracy. Using the consensus spectra reported by msCRUSH, commonly used spectra search engines MSGF+ and Mascot can identify 3 and 1% more unique peptides, respectively, compared with the identification results from the raw MS/MS spectra at the same false discovery rate (1% FDR) of peptide level. msCRUSH is implemented in C++ and is released as open-source software.
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Affiliation(s)
- Lei Wang
- School of Informatics, Computing and Engineering , Indiana University , Bloomington , Indiana 47408 , United States
| | - Sujun Li
- School of Informatics, Computing and Engineering , Indiana University , Bloomington , Indiana 47408 , United States
| | - Haixu Tang
- School of Informatics, Computing and Engineering , Indiana University , Bloomington , Indiana 47408 , United States
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Reconstructing phosphorylation signalling networks from quantitative phosphoproteomic data. Essays Biochem 2018; 62:525-534. [PMID: 30072490 PMCID: PMC6204553 DOI: 10.1042/ebc20180019] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 06/25/2018] [Accepted: 06/26/2018] [Indexed: 12/25/2022]
Abstract
Cascades of phosphorylation between protein kinases comprise a core mechanism in the integration and propagation of intracellular signals. Although we have accumulated a wealth of knowledge around some such pathways, this is subject to study biases and much remains to be uncovered. Phosphoproteomics, the identification and quantification of phosphorylated proteins on a proteomic scale, provides a high-throughput means of interrogating the state of intracellular phosphorylation, both at the pathway level and at the whole-cell level. In this review, we discuss methods for using human quantitative phosphoproteomic data to reconstruct the underlying signalling networks that generated it. We address several challenges imposed by the data on such analyses and we consider promising advances towards reconstructing unbiased, kinome-scale signalling networks.
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Watson J, Francavilla C. Regulation of FGF10 Signaling in Development and Disease. Front Genet 2018; 9:500. [PMID: 30405705 PMCID: PMC6205963 DOI: 10.3389/fgene.2018.00500] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 10/05/2018] [Indexed: 12/12/2022] Open
Abstract
Fibroblast Growth Factor 10 (FGF10) is a multifunctional mesenchymal-epithelial signaling growth factor, which is essential for multi-organ development and tissue homeostasis in adults. Furthermore, FGF10 deregulation has been associated with human genetic disorders and certain forms of cancer. Upon binding to FGF receptors with heparan sulfate as co-factor, FGF10 activates several intracellular signaling cascades, resulting in cell proliferation, differentiation, and invasion. FGF10 activity is modulated not only by heparan sulfate proteoglycans in the extracellular matrix, but also by hormones and other soluble factors. Despite more than 20 years of research on FGF10 functions, context-dependent regulation of FGF10 signaling specificity remains poorly understood. Emerging modes of FGF10 signaling regulation will be described, focusing on the role of FGF10 trafficking and sub-cellular localization, heparan sulfate proteoglycans, and miRNAs. Systems biology approaches based on quantitative proteomics will be considered for globally investigating FGF10 signaling specificity. Finally, current gaps in our understanding of FGF10 functions, such as the relative contribution of receptor isoforms to signaling activation, will be discussed in the context of genetic disorders and tumorigenesis.
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Affiliation(s)
- Joanne Watson
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester, United Kingdom
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Chiara Francavilla
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester, United Kingdom
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Floriou-Servou A, von Ziegler L, Stalder L, Sturman O, Privitera M, Rassi A, Cremonesi A, Thöny B, Bohacek J. Distinct Proteomic, Transcriptomic, and Epigenetic Stress Responses in Dorsal and Ventral Hippocampus. Biol Psychiatry 2018; 84:531-541. [PMID: 29605177 DOI: 10.1016/j.biopsych.2018.02.003] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 01/24/2018] [Accepted: 02/05/2018] [Indexed: 12/27/2022]
Abstract
BACKGROUND Acutely stressful experiences can trigger neuropsychiatric disorders and impair cognitive processes by altering hippocampal function. Although the intrinsic organization of the hippocampus is highly conserved throughout its long dorsal-ventral axis, the dorsal (anterior) hippocampus mediates spatial navigation and memory formation, whereas the ventral (posterior) hippocampus is involved in emotion regulation. To understand the molecular consequences of stress, detailed genome-wide screens are necessary and need to distinguish between dorsal and ventral hippocampal regions. While transcriptomic screens have become a mainstay in basic and clinical research, proteomic methods are rapidly evolving and hold even greater promise to reveal biologically and clinically relevant biomarkers. METHODS Here, we provide the first combined transcriptomic (RNA sequencing) and proteomic (sequential window acquisition of all theoretical mass spectra [SWATH-MS]) profiling of dorsal and ventral hippocampus in mice. We used three different acute stressors (novelty, swim, and restraint) to assess the impact of stress on both regions. RESULTS We demonstrated that both hippocampal regions display radically distinct molecular responses and that the ventral hippocampus is particularly sensitive to the effects of stress. Separately analyzing these structures greatly increased the sensitivity to detect stress-induced changes. For example, protein interaction cluster analyses revealed a stress-responsive epigenetic network around histone demethylase Kdm6b restricted to the ventral hippocampus, and acute stress reduced methylation of its enzymatic target H3K27me3. Selective Kdm6b knockdown in the ventral hippocampus led to behavioral hyperactivity/hyperresponsiveness. CONCLUSIONS These findings underscore the importance of considering dorsal and ventral hippocampus separately when conducting high-throughput molecular analyses, which has important implications for fundamental research as well as clinical studies.
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Affiliation(s)
- Amalia Floriou-Servou
- Laboratory of Molecular and Behavioral Neuroscience, Department of Health Science and Technology of ETH Zurich, Institute for Neuroscience, Neuroscience Center Zurich, Zurich, Switzerland
| | - Lukas von Ziegler
- Laboratory of Molecular and Behavioral Neuroscience, Department of Health Science and Technology of ETH Zurich, Institute for Neuroscience, Neuroscience Center Zurich, Zurich, Switzerland; Laboratory of Neuroepigenetics, Medical Faculty of the University Zürich and Department of Health Science and Technology of the ETH Zürich, Zurich, Switzerland
| | - Luzia Stalder
- Laboratory of Neuroepigenetics, Medical Faculty of the University Zürich and Department of Health Science and Technology of the ETH Zürich, Zurich, Switzerland
| | - Oliver Sturman
- Laboratory of Molecular and Behavioral Neuroscience, Department of Health Science and Technology of ETH Zurich, Institute for Neuroscience, Neuroscience Center Zurich, Zurich, Switzerland
| | - Mattia Privitera
- Laboratory of Molecular and Behavioral Neuroscience, Department of Health Science and Technology of ETH Zurich, Institute for Neuroscience, Neuroscience Center Zurich, Zurich, Switzerland
| | - Anahita Rassi
- Division of Clinical Chemistry and Biochemistry, University Children's Hospital Zurich, Zurich, Switzerland
| | - Alessio Cremonesi
- Division of Clinical Chemistry and Biochemistry, University Children's Hospital Zurich, Zurich, Switzerland
| | - Beat Thöny
- Division of Metabolism, University Children's Hospital Zurich, Zurich, Switzerland
| | - Johannes Bohacek
- Laboratory of Molecular and Behavioral Neuroscience, Department of Health Science and Technology of ETH Zurich, Institute for Neuroscience, Neuroscience Center Zurich, Zurich, Switzerland.
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36
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Titz B, Gadaleta RM, Lo Sasso G, Elamin A, Ekroos K, Ivanov NV, Peitsch MC, Hoeng J. Proteomics and Lipidomics in Inflammatory Bowel Disease Research: From Mechanistic Insights to Biomarker Identification. Int J Mol Sci 2018; 19:ijms19092775. [PMID: 30223557 PMCID: PMC6163330 DOI: 10.3390/ijms19092775] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 09/11/2018] [Accepted: 09/12/2018] [Indexed: 02/06/2023] Open
Abstract
Inflammatory bowel disease (IBD) represents a group of progressive disorders characterized by recurrent chronic inflammation of the gut. Ulcerative colitis and Crohn's disease are the major manifestations of IBD. While our understanding of IBD has progressed in recent years, its etiology is far from being fully understood, resulting in suboptimal treatment options. Complementing other biological endpoints, bioanalytical "omics" methods that quantify many biomolecules simultaneously have great potential in the dissection of the complex pathogenesis of IBD. In this review, we focus on the rapidly evolving proteomics and lipidomics technologies and their broad applicability to IBD studies; these range from investigations of immune-regulatory mechanisms and biomarker discovery to studies dissecting host⁻microbiome interactions and the role of intestinal epithelial cells. Future studies can leverage recent advances, including improved analytical methodologies, additional relevant sample types, and integrative multi-omics analyses. Proteomics and lipidomics could effectively accelerate the development of novel targeted treatments and the discovery of complementary biomarkers, enabling continuous monitoring of the treatment response of individual patients; this may allow further refinement of treatment and, ultimately, facilitate a personalized medicine approach to IBD.
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Affiliation(s)
- Bjoern Titz
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchatel, Switzerland.
| | - Raffaella M Gadaleta
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchatel, Switzerland.
| | - Giuseppe Lo Sasso
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchatel, Switzerland.
| | - Ashraf Elamin
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchatel, Switzerland.
| | - Kim Ekroos
- Lipidomics Consulting Ltd., Irisviksvägen 31D, 02230 Esbo, Finland.
| | - Nikolai V Ivanov
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchatel, Switzerland.
| | - Manuel C Peitsch
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchatel, Switzerland.
| | - Julia Hoeng
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchatel, Switzerland.
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37
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Exploration of variations in proteome and metabolome for predictive diagnostics and personalized treatment algorithms: Innovative approach and examples for potential clinical application. J Proteomics 2018; 188:30-40. [DOI: 10.1016/j.jprot.2017.08.020] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 08/06/2017] [Accepted: 08/25/2017] [Indexed: 12/20/2022]
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38
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Kawasaki A, Okada M, Tamada A, Okuda S, Nozumi M, Ito Y, Kobayashi D, Yamasaki T, Yokoyama R, Shibata T, Nishina H, Yoshida Y, Fujii Y, Takeuchi K, Igarashi M. Growth Cone Phosphoproteomics Reveals that GAP-43 Phosphorylated by JNK Is a Marker of Axon Growth and Regeneration. iScience 2018; 4:190-203. [PMID: 30240740 PMCID: PMC6147025 DOI: 10.1016/j.isci.2018.05.019] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 05/05/2018] [Accepted: 05/25/2018] [Indexed: 12/20/2022] Open
Abstract
Neuronal growth cones are essential for nerve growth and regeneration, as well as for the formation and rearrangement of the neural network. To elucidate phosphorylation-dependent signaling pathways and establish useful molecular markers for axon growth and regeneration, we performed a phosphoproteomics study of mammalian growth cones, which identified >30,000 phosphopeptides of ∼1,200 proteins. The phosphorylation sites were highly proline directed and primarily MAPK dependent, owing to the activation of JNK, suggesting that proteins that undergo proline-directed phosphorylation mediate nerve growth in the mammalian brain. Bioinformatics analysis revealed that phosphoproteins were enriched in microtubules and the cortical cytoskeleton. The most frequently phosphorylated site was S96 of GAP-43 (growth-associated protein 43-kDa), a vertebrate-specific protein involved in axon growth. This previously uncharacterized phosphorylation site was JNK dependent. S96 phosphorylation was specifically detected in growing and regenerating axons as the most frequent target of JNK signaling; thus it represents a promising new molecular marker for mammalian axonal growth and regeneration. Phosphoproteomics of mammalian growth cone membranes reveals activation of MAPK JNK is the activated MAPK in growth cones and phosphorylates S96 of GAP-43 pS96 of GAP-43, the most frequent site, is observed in growing axons pS96 is biochemically detected in the regenerating axons of the peripheral nerves
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Affiliation(s)
- Asami Kawasaki
- Department of Neurochemistry and Molecular Cell Biology, Graduate School of Medical and Dental Sciences, Niigata University, 1-757 Asahimachi, Chuo-ku, Niigata 951-8510, Japan; Center for Trans-disciplinary Research, Institute for Research Promotion, Niigata University, Chuo-ku, Niigata 951-8510, Japan
| | - Masayasu Okada
- Department of Neurochemistry and Molecular Cell Biology, Graduate School of Medical and Dental Sciences, Niigata University, 1-757 Asahimachi, Chuo-ku, Niigata 951-8510, Japan; Center for Trans-disciplinary Research, Institute for Research Promotion, Niigata University, Chuo-ku, Niigata 951-8510, Japan; Department of Neurosurgery, Brain Research Institute, Niigata University, Chuo-ku, Niigata 951-8585, Japan
| | - Atsushi Tamada
- Department of Neurochemistry and Molecular Cell Biology, Graduate School of Medical and Dental Sciences, Niigata University, 1-757 Asahimachi, Chuo-ku, Niigata 951-8510, Japan; Center for Trans-disciplinary Research, Institute for Research Promotion, Niigata University, Chuo-ku, Niigata 951-8510, Japan; Precursory Research for Embryonic Science and Technology, Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012, Japan
| | - Shujiro Okuda
- Laboratory of Bioinformatics, Graduate School of Medical and Dental Sciences, Niigata University, Chuo-ku, Niigata 951-8510, Japan
| | - Motohiro Nozumi
- Department of Neurochemistry and Molecular Cell Biology, Graduate School of Medical and Dental Sciences, Niigata University, 1-757 Asahimachi, Chuo-ku, Niigata 951-8510, Japan; Center for Trans-disciplinary Research, Institute for Research Promotion, Niigata University, Chuo-ku, Niigata 951-8510, Japan
| | - Yasuyuki Ito
- Department of Neurochemistry and Molecular Cell Biology, Graduate School of Medical and Dental Sciences, Niigata University, 1-757 Asahimachi, Chuo-ku, Niigata 951-8510, Japan
| | - Daiki Kobayashi
- Department of Neurochemistry and Molecular Cell Biology, Graduate School of Medical and Dental Sciences, Niigata University, 1-757 Asahimachi, Chuo-ku, Niigata 951-8510, Japan
| | - Tokiwa Yamasaki
- Department of Developmental and Regenerative Biology, Medical Research Institute, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Ryo Yokoyama
- K.K. Sciex Japan, Shinagawa-ku, Tokyo 140-0001, Japan
| | | | - Hiroshi Nishina
- Department of Developmental and Regenerative Biology, Medical Research Institute, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Yutaka Yoshida
- Center for Coordination of Research, Institute for Research Promotion, Niigata University, Ikarashi, Niigata 951-2181, Japan
| | - Yukihiko Fujii
- Department of Neurosurgery, Brain Research Institute, Niigata University, Chuo-ku, Niigata 951-8585, Japan
| | - Kosei Takeuchi
- Department of Neurochemistry and Molecular Cell Biology, Graduate School of Medical and Dental Sciences, Niigata University, 1-757 Asahimachi, Chuo-ku, Niigata 951-8510, Japan; Center for Trans-disciplinary Research, Institute for Research Promotion, Niigata University, Chuo-ku, Niigata 951-8510, Japan; Department of Medical Cell Biology, Aichi Medical University, Nagakute, Aichi 480-1195, Japan
| | - Michihiro Igarashi
- Department of Neurochemistry and Molecular Cell Biology, Graduate School of Medical and Dental Sciences, Niigata University, 1-757 Asahimachi, Chuo-ku, Niigata 951-8510, Japan; Center for Trans-disciplinary Research, Institute for Research Promotion, Niigata University, Chuo-ku, Niigata 951-8510, Japan.
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39
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Strand NS, Allen JM, Zayas RM. Post-translational regulation of planarian regeneration. Semin Cell Dev Biol 2018; 87:58-68. [PMID: 29705300 DOI: 10.1016/j.semcdb.2018.04.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 04/24/2018] [Accepted: 04/25/2018] [Indexed: 02/07/2023]
Abstract
Most mammals cannot easily overcome degenerative disease or traumatic injuries. In contrast, an innate ability to regenerate is observed across animal phyla. Freshwater planarians are amongst the organisms that are capable of stem cell-mediated whole-body regeneration and have served as an exemplary model to study how pluripotency is maintained and regulated in vivo. Here, we review findings on the role of post-translational modifications and the genes regulating phosphorylation, ubiquitylation, and chromatin remodeling in planarian regeneration. Furthermore, we discuss how technological advances for identifying cellular targets of these processes will fill gaps in our knowledge of the signaling mechanisms that underlie regeneration in planarians, which should inform how tissue repair can be stimulated in non-regenerative model organisms and in humans.
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Affiliation(s)
- Nicholas S Strand
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
| | - John M Allen
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
| | - Ricardo M Zayas
- Department of Biology, San Diego State University, San Diego, CA 92182, USA.
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40
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Affiliation(s)
- Nicholas
M. Riley
- Department
of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Genome
Center of Wisconsin, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Joshua J. Coon
- Department
of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Genome
Center of Wisconsin, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department
of Biomolecular Chemistry, University of
Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Morgridge
Institute for Research, Madison, Wisconsin 53715, United States
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41
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Lombardi B, Ashford P, Moya-Garcia AA, Rust A, Crawford M, Williams SV, Knowles MA, Katan M, Orengo C, Godovac-Zimmermann J. Unique signalling connectivity of FGFR3-TACC3 oncoprotein revealed by quantitative phosphoproteomics and differential network analysis. Oncotarget 2017; 8:102898-102911. [PMID: 29262532 PMCID: PMC5732698 DOI: 10.18632/oncotarget.22048] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 10/03/2017] [Indexed: 12/14/2022] Open
Abstract
The FGFR3-TACC3 fusion is an oncogenic driver in diverse malignancies, including bladder cancer, characterized by upregulated tyrosine kinase activity. To gain insights into distinct properties of FGFR3-TACC3 down-stream signalling, we utilised telomerase-immortalised normal human urothelial cell lines expressing either the fusion or wild-type FGFR3 (isoform IIIb) for subsequent quantitative proteomics and network analysis. Cellular lysates were chemically labelled with isobaric tandem mass tag reagents and, after phosphopeptide enrichment, liquid chromatography-high mass accuracy tandem mass spectrometry (LC-MS/MS) was used for peptide identification and quantification. Comparison of data from the two cell lines under non-stimulated and FGF1 stimulated conditions and of data representing physiological stimulation of FGFR3 identified about 200 regulated phosphosites. The identified phosphoproteins and quantified phosphosites were further analysed in the context of functional biological networks by inferring kinase-substrate interactions, mapping these to a comprehensive human signalling interaction network, filtering based on tissue-expression profiles and applying disease module detection and pathway enrichment methods. Analysis of our phosphoproteomics data using these bioinformatics methods combined into a new protocol-Disease Relevant Analysis of Genes On Networks (DRAGON)-allowed us to tease apart pathways differentially involved in FGFR3-TACC3 signalling in comparison to wild-type FGFR3 and to investigate their local phospho-signalling context. We highlight 9 pathways significantly regulated only in the cell line expressing FGFR3-TACC3 fusion and 5 pathways regulated only by stimulation of the wild-type FGFR3. Pathways differentially linked to FGFR3-TACC3 fusion include those related to chaperone activation and stress response and to regulation of TP53 expression and degradation that could contribute to development and maintenance of the cancer phenotype.
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Affiliation(s)
- Benedetta Lombardi
- Proteomics and Molecular Cell Dynamics, Center for Nephrology, School of Life and Medical Sciences, University College London, London NW3 2PF, United Kingdom
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom
| | - Paul Ashford
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom
| | - Aurelio A. Moya-Garcia
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom
| | - Aleksander Rust
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom
| | - Mark Crawford
- Proteomics and Molecular Cell Dynamics, Center for Nephrology, School of Life and Medical Sciences, University College London, London NW3 2PF, United Kingdom
| | - Sarah V. Williams
- Section of Molecular Oncology, Leeds Institute of Molecular Medicine, St James’s University Hospital, Leeds LS9 7TF, United Kingdom
| | - Margaret A. Knowles
- Section of Molecular Oncology, Leeds Institute of Molecular Medicine, St James’s University Hospital, Leeds LS9 7TF, United Kingdom
| | - Matilda Katan
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom
| | - Christine Orengo
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom
| | - Jasminka Godovac-Zimmermann
- Proteomics and Molecular Cell Dynamics, Center for Nephrology, School of Life and Medical Sciences, University College London, London NW3 2PF, United Kingdom
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42
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Phosphoproteomics of Primary Cells Reveals Druggable Kinase Signatures in Ovarian Cancer. Cell Rep 2017; 18:3242-3256. [PMID: 28355574 PMCID: PMC5382236 DOI: 10.1016/j.celrep.2017.03.015] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 01/04/2017] [Accepted: 03/02/2017] [Indexed: 12/20/2022] Open
Abstract
Our understanding of the molecular determinants of cancer is still inadequate because of cancer heterogeneity. Here, using epithelial ovarian cancer (EOC) as a model system, we analyzed a minute amount of patient-derived epithelial cells from either healthy or cancerous tissues by single-shot mass-spectrometry-based phosphoproteomics. Using a multi-disciplinary approach, we demonstrated that primary cells recapitulate tissue complexity and represent a valuable source of differentially expressed proteins and phosphorylation sites that discriminate cancer from healthy cells. Furthermore, we uncovered kinase signatures associated with EOC. In particular, CDK7 targets were characterized in both EOC primary cells and ovarian cancer cell lines. We showed that CDK7 controls cell proliferation and that pharmacological inhibition of CDK7 selectively represses EOC cell proliferation. Our approach defines the molecular landscape of EOC, paving the way for efficient therapeutic approaches for patients. Finally, we highlight the potential of phosphoproteomics to identify clinically relevant and druggable pathways in cancer. We analyze ex-vivo-cultured primary cells using phosphoproteomics We investigate epithelial ovarian cancer (EOC) and healthy tissue We uncover expression of cancer-specific proteins and kinase signatures The kinase CDK7 phosphorylates POLR2A and regulates EOC cell proliferation
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43
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Flores-Morales A, Iglesias-Gato D. Quantitative Mass Spectrometry-Based Proteomic Profiling for Precision Medicine in Prostate Cancer. Front Oncol 2017; 7:267. [PMID: 29164064 PMCID: PMC5674010 DOI: 10.3389/fonc.2017.00267] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 10/23/2017] [Indexed: 12/12/2022] Open
Abstract
Prostate cancer (PCa) is one of the most frequently diagnosed cancer among men in the western societies. Many PCa patients bear tumors that will not threat their lives if left untreated or if treatment is delayed. Our inability for early identification of these patients has resulted in massive overtreatment. Therefore, there is a great need of finding biomarkers for patient stratification according to prognostic risk; as well as there is a need for novel targets that can allow the development of effective treatments for patients that progress to castration-resistant PCa. Most biomarkers in cancer are proteins, including the widely-used prostate-specific antigen (PSA). Recent developments in mass spectrometry allow the identification and quantification of thousands of proteins and posttranslational modifications from small amounts of biological material, including formalin-fixed paraffin-embedded tissues, and biological fluids. Novel diagnostic and prognostic biomarkers have been identified in tissue, blood, urine, and seminal plasma of PCa patients, and new insights in the ethology and progression of this disease have been achieved using this technology. In this review, we summarize these findings and discuss the potential of this technology to pave the way toward the clinical implementation of precision medicine in PCa.
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Affiliation(s)
- Amilcar Flores-Morales
- Faculty of Health and Medical Sciences, Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark.,Danish Cancer Society Research Center, Danish Cancer Society, Copenhagen, Denmark
| | - Diego Iglesias-Gato
- Faculty of Health and Medical Sciences, Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark.,Danish Cancer Society Research Center, Danish Cancer Society, Copenhagen, Denmark
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44
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Hayashi K, Yamashita R, Takami R, Matsui T, Gotou M, Nishimoto T, Kobayashi H. Strategy for Identification of Phosphorylation Levels of Low Abundance Proteins in Vivo for Which Antibodies Are not Available. J Cardiovasc Dev Dis 2017; 4:jcdd4040017. [PMID: 29367546 PMCID: PMC5753118 DOI: 10.3390/jcdd4040017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 09/22/2017] [Accepted: 09/30/2017] [Indexed: 12/05/2022] Open
Abstract
Protein function is mainly modulated by dynamic reversible or irreversible post-translational modifications. Among them, the identification of protein phosphorylation sites and changes in phosphorylation levels in vivo are of considerable interest for a better understanding of the protein function. Thus, effective strategies for the quantitative determination of phosphorylation degrees for low abundant proteins, for which antibodies are not available, are required in order to evaluate the functional regulation of proteins attributed to phosphorylation. In this study, we used the heart β1-adrenergic receptor (Adrb1) as a model protein and developed FLAG-Adrb1 knock-in mice, in which the FLAG tag was inserted at the N-terminus of Adrb1. The phosphorylation sites and levels of Adrb1 in the heart were elucidated by immuno-affinity purification followed by quantitative mass spectrometry analysis using ion intensity ratio of the phosphorylated peptide versus corresponding unphosphorylated peptide. The phosphorylation levels at Ser274 and Ser462 of Adrb1 were approximately 0.25 and 0.0023. This effective strategy should be useful for not only analyzing site-specific phosphorylation levels of target proteins, but also quantifying the expression levels of proteins of interest when appropriate antibodies are not available.
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Affiliation(s)
- Kozo Hayashi
- Integrated Technology Research Laboratories, Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, Kanagawa 251-8555 Fujisawa, Japan.
| | - Ryo Yamashita
- Integrated Technology Research Laboratories, Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, Kanagawa 251-8555 Fujisawa, Japan.
| | - Ritsuko Takami
- Integrated Technology Research Laboratories, Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, Kanagawa 251-8555 Fujisawa, Japan.
| | - Toshikatsu Matsui
- Cardiovascular and Metabolic Drug Discovery Unit, Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, Kanagawa 251-8555 Fujisawa, Japan.
| | - Masamitsu Gotou
- Integrated Technology Research Laboratories, Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, Kanagawa 251-8555 Fujisawa, Japan.
| | - Tomoyuki Nishimoto
- Cardiovascular and Metabolic Drug Discovery Unit, Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, Kanagawa 251-8555 Fujisawa, Japan.
| | - Hiroyuki Kobayashi
- Integrated Technology Research Laboratories, Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, Kanagawa 251-8555 Fujisawa, Japan.
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45
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Álvarez-Salamero C, Castillo-González R, Navarro MN. Lighting Up T Lymphocyte Signaling with Quantitative Phosphoproteomics. Front Immunol 2017; 8:938. [PMID: 28848546 PMCID: PMC5552657 DOI: 10.3389/fimmu.2017.00938] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 07/21/2017] [Indexed: 12/31/2022] Open
Abstract
Phosphorylation is the most abundant post-translational modification, regulating several aspects of protein and cell function. Quantitative phosphoproteomics approaches have expanded the scope of phosphorylation analysis enabling the quantification of changes in thousands of phosphorylation sites simultaneously in two or more conditions. These approaches offer a global view of the impact of cellular perturbations such as extracellular stimuli or gene ablation in intracellular signaling networks. Such great potential also brings on a new challenge: to identify, among the thousands of phosphorylations found in global phosphoproteomics studies, the small subset of site-specific phosphorylations expected to be functionally relevant. This review focus on updating and integrating findings on T lymphocyte signaling generated using global phosphoproteomics approaches, drawing attention on the biological relevance of the obtained data.
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Affiliation(s)
- Candelas Álvarez-Salamero
- Departamento de Medicina, Universidad Autónoma de Madrid, Madrid, Spain.,Instituto de Investigación Sanitaria del Hospital Universitario de La Princesa, Madrid, Spain
| | | | - María N Navarro
- Departamento de Medicina, Universidad Autónoma de Madrid, Madrid, Spain.,Instituto de Investigación Sanitaria del Hospital Universitario de La Princesa, Madrid, Spain.,Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Madrid, Spain
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46
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The role of mass spectrometry analysis in bacterial effector characterization. Biochem J 2017; 474:2779-2784. [DOI: 10.1042/bcj20160797] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2017] [Revised: 06/26/2017] [Accepted: 07/06/2017] [Indexed: 12/20/2022]
Abstract
Many secreted bacterial effector proteins play a critical role in host–pathogen interactions by mediating a variety of post-translational modifications, some of which do not occur natively within the eukaryotic proteome. The characterization of bacterial effector protein activity remains an important step to understanding the subversion of host cell biology during pathogen infection and although molecular biology and immunochemistry remain critical tools for gaining insights into bacterial effector functions, increasingly mass spectrometry (MS) and proteomic approaches are also playing an indispensable role. The focus of this editorial is to highlight the strengths of specific MS approaches and their utility for the characterization of bacterial effector activity. With the capability of new generation MS instrumentation, MS-based technologies can provide information that is inaccessible using traditional molecular or immunochemical approaches.
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47
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Abstract
Viral infections are a major burden to human and animal health. Immune response against viruses consists of innate and adaptive immunity which are both critical for the eradication of the viral infection. The innate immune system is the first line of defense against viral infections. Proper innate immune response is required for the activation of adaptive, humoral and cell-mediated immunity. Macrophages are innate immune cells which have a central role in detecting viral infections including influenza A and human immunodeficiency viruses. Macrophages and other host cells respond to viral infection by modulating their protein expression levels, proteins' posttranslational modifications, as well as proteins' intracellular localization and secretion. Therefore the detailed characterization how viruses dynamically manipulate host proteome is needed for understanding the molecular mechanisms of viral infection. It is critical to identify cellular host factors which are exploited by different viruses, and which are less prone for mutations and could serve as potential targets for novel antiviral compounds. Here, we review how proteomics studies have enhanced our understanding of macrophage response to viral infection with special focus on Influenza A and Human immunodeficiency viruses, and virus infections of swine. SIGNIFICANCE Influenza A viruses (IAVs) and human immunodeficiency viruses (HIV) infect annually millions of people worldwide and they form a severe threat to human health. Both IAVs and HIV-1 can efficiently antagonize host response and develop drug-resistant variants. Most current antiviral drugs are directed against viral proteins, and there is a constant need to develop new next-generation drugs targeting host proteins that are essential for viral replication. Porcine reproductive and respiratory syndrome virus (PRRSV) and porcine circovirus type 2 (PCV2) are economically important swine pathogens. Both PRRSV and PCV2 cause severe respiratory tract illnesses in swine. IAVs, HIV-1, and swine viruses infect macrophages activating antiviral response against these viruses. Macrophages also have a central role in the replication and spread of these viruses. However, macrophage response to these viruses is incompletely understood. Current proteomics methods can provide a global view of host-response to viral infection which is needed for in-depth understanding the molecular mechanisms of viral infection. Here we review the current proteomics studies on macrophage response to viral infection and provide insight into the global host proteome changes upon viral infection.
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Affiliation(s)
- Tuula A Nyman
- Department of Immunology, Institute of Clinical Medicine, University of Oslo and Rikshospitalet Oslo, Oslo, Norway.
| | - Sampsa Matikainen
- University of Helsinki and Helsinki University Hospital, Rheumatology, Helsinki, Finland
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48
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Riley NM, Hebert AS, Dürnberger G, Stanek F, Mechtler K, Westphall MS, Coon JJ. Phosphoproteomics with Activated Ion Electron Transfer Dissociation. Anal Chem 2017; 89:6367-6376. [PMID: 28383256 PMCID: PMC5555596 DOI: 10.1021/acs.analchem.7b00212] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The ability to localize phosphosites to specific amino acid residues is crucial to translating phosphoproteomic data into biological meaningful contexts. In a companion manuscript ( Anal. Chem. 2017 , DOI: 10.1021/acs.analchem.7b00213 ), we described a new implementation of activated ion electron transfer dissociation (AI-ETD) on a quadrupole-Orbitrap-linear ion trap hybrid MS system (Orbitrap Fusion Lumos), which greatly improved peptide fragmentation and identification over ETD and other supplemental activation methods. Here we present the performance of AI-ETD for identifying and localizing sites of phosphorylation in both phosphopeptides and intact phosphoproteins. Using 90 min analyses we show that AI-ETD can identify 24,503 localized phosphopeptide spectral matches enriched from mouse brain lysates, which more than triples identifications from standard ETD experiments and outperforms ETcaD and EThcD as well. AI-ETD achieves these gains through improved quality of fragmentation and MS/MS success rates for all precursor charge states, especially for doubly protonated species. We also evaluate the degree to which phosphate neutral loss occurs from phosphopeptide product ions due to the infrared photoactivation of AI-ETD and show that modifying phosphoRS (a phosphosite localization algorithm) to include phosphate neutral losses can significantly improve localization in AI-ETD spectra. Finally, we demonstrate the utility of AI-ETD in localizing phosphosites in α-casein, an ∼23.5 kDa phosphoprotein that showed eight of nine known phosphorylation sites occupied upon intact mass analysis. AI-ETD provided the greatest sequence coverage for all five charge states investigated and was the only fragmentation method to localize all eight phosphosites for each precursor. Overall, this work highlights the analytical value AI-ETD can bring to both bottom-up and top-down phosphoproteomics.
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Affiliation(s)
- Nicholas M. Riley
- Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Alexander S. Hebert
- Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Gerhard Dürnberger
- Institute of Molecular Pathology (IMP), Campus-Vienna-Biocenter 1, A-1030 Vienna, Austria
- GMI, Gregor Mendel Institute of Molecular Plant Biology, Dr. Bohr Gasse 3, A-1030 Vienna, Austria
- IMBA, Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Dr. Bohr Gasse 3, A-1030 Vienna, Austria
| | - Florian Stanek
- Institute of Molecular Pathology (IMP), Campus-Vienna-Biocenter 1, A-1030 Vienna, Austria
| | - Karl Mechtler
- Institute of Molecular Pathology (IMP), Campus-Vienna-Biocenter 1, A-1030 Vienna, Austria
- IMBA, Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Dr. Bohr Gasse 3, A-1030 Vienna, Austria
| | - Michael S. Westphall
- Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Joshua J. Coon
- Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Morgridge Institute for Research, Madison, Wisconsin, USA
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49
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Bekker-Jensen DB, Kelstrup CD, Batth TS, Larsen SC, Haldrup C, Bramsen JB, Sørensen KD, Høyer S, Ørntoft TF, Andersen CL, Nielsen ML, Olsen JV. An Optimized Shotgun Strategy for the Rapid Generation of Comprehensive Human Proteomes. Cell Syst 2017; 4:587-599.e4. [PMID: 28601559 PMCID: PMC5493283 DOI: 10.1016/j.cels.2017.05.009] [Citation(s) in RCA: 305] [Impact Index Per Article: 43.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 03/03/2017] [Accepted: 05/11/2017] [Indexed: 01/08/2023]
Abstract
This study investigates the challenge of comprehensively cataloging the complete human proteome from a single-cell type using mass spectrometry (MS)-based shotgun proteomics. We modify a classical two-dimensional high-resolution reversed-phase peptide fractionation scheme and optimize a protocol that provides sufficient peak capacity to saturate the sequencing speed of modern MS instruments. This strategy enables the deepest proteome of a human single-cell type to date, with the HeLa proteome sequenced to a depth of ∼584,000 unique peptide sequences and ∼14,200 protein isoforms (∼12,200 protein-coding genes). This depth is comparable with next-generation RNA sequencing and enables the identification of post-translational modifications, including ∼7,000 N-acetylation sites and ∼10,000 phosphorylation sites, without the need for enrichment. We further demonstrate the general applicability and clinical potential of this proteomics strategy by comprehensively quantifying global proteome expression in several different human cancer cell lines and patient tissue samples. Multi-shot proteomics quantifies the protein levels of 12,200+ genes in HeLa cells This essentially complete HeLa proteome has coverage similar to next-gen RNA-seq Deep coverage of major PTMs is achieved without specific enrichment The approach is extendable to other human cell lines and patient samples
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Affiliation(s)
- Dorte B Bekker-Jensen
- Proteomics Program, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Christian D Kelstrup
- Proteomics Program, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark.
| | - Tanveer S Batth
- Proteomics Program, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Sara C Larsen
- Proteomics Program, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Christa Haldrup
- Departments of Molecular Medicine and Clinical Medicine, Aarhus University Hospital, Aarhus University, Palle Juul-Jensens Boulevard 99, 8200 Aarhus, Denmark
| | - Jesper B Bramsen
- Departments of Molecular Medicine and Clinical Medicine, Aarhus University Hospital, Aarhus University, Palle Juul-Jensens Boulevard 99, 8200 Aarhus, Denmark
| | - Karina D Sørensen
- Departments of Molecular Medicine and Clinical Medicine, Aarhus University Hospital, Aarhus University, Palle Juul-Jensens Boulevard 99, 8200 Aarhus, Denmark
| | - Søren Høyer
- Institute of Pathology, Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, 8200 Aarhus, Denmark
| | - Torben F Ørntoft
- Departments of Molecular Medicine and Clinical Medicine, Aarhus University Hospital, Aarhus University, Palle Juul-Jensens Boulevard 99, 8200 Aarhus, Denmark
| | - Claus L Andersen
- Departments of Molecular Medicine and Clinical Medicine, Aarhus University Hospital, Aarhus University, Palle Juul-Jensens Boulevard 99, 8200 Aarhus, Denmark
| | - Michael L Nielsen
- Proteomics Program, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Jesper V Olsen
- Proteomics Program, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark.
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50
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Henry M, Power M, Kaushik P, Coleman O, Clynes M, Meleady P. Differential Phosphoproteomic Analysis of Recombinant Chinese Hamster Ovary Cells Following Temperature Shift. J Proteome Res 2017; 16:2339-2358. [DOI: 10.1021/acs.jproteome.6b00868] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Michael Henry
- National Institute for Cellular
Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Martin Power
- National Institute for Cellular
Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Prashant Kaushik
- National Institute for Cellular
Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Orla Coleman
- National Institute for Cellular
Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Martin Clynes
- National Institute for Cellular
Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Paula Meleady
- National Institute for Cellular
Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
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