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Lyu J, Wang K, Ye M. Modification-free approaches to screen drug targets at proteome level. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2019.06.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Cost-effective generation of precise label-free quantitative proteomes in high-throughput by microLC and data-independent acquisition. Sci Rep 2018. [PMID: 29531254 PMCID: PMC5847575 DOI: 10.1038/s41598-018-22610-4] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Quantitative proteomics is key for basic research, but needs improvements to satisfy an increasing demand for large sample series in diagnostics, academia and industry. A switch from nanoflowrate to microflowrate chromatography can improve throughput and reduce costs. However, concerns about undersampling and coverage have so far hampered its broad application. We used a QTOF mass spectrometer of the penultimate generation (TripleTOF5600), converted a nanoLC system into a microflow platform, and adapted a SWATH regime for large sample series by implementing retention time- and batch correction strategies. From 3 µg to 5 µg of unfractionated tryptic digests that are obtained from proteomics-typical amounts of starting material, microLC-SWATH-MS quantifies up to 4000 human or 1750 yeast proteins in an hour or less. In the acquisition of 750 yeast proteomes, retention times varied between 2% and 5%, and quantified the typical peptide with 5–8% signal variation in replicates, and below 20% in samples acquired over a five-months period. Providing precise quantities without being dependent on the latest hardware, our study demonstrates that the combination of microflow chromatography and data-independent acquisition strategies has the potential to overcome current bottlenecks in academia and industry, enabling the cost-effective generation of precise quantitative proteomes in large scale.
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Ravindran MS, Wenk MR. Activity-Based Lipid Esterase Profiling of M. bovis BCG at Different Metabolic States Using Tetrahydrolipstatin (THL) as Bait. Methods Mol Biol 2018; 1491:75-85. [PMID: 27778282 DOI: 10.1007/978-1-4939-6439-0_6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
This chapter provides a step-by-step protocol using activity-based protein profiling (ABPP) as a chemical-proteomic tool to survey the antibiotic properties of a small molecule. Here, we investigate the molecular mechanism behind the bactericidal activity of tetrahydrolipstatin (THL). ABPP relies on small molecule probes that target the active site of specific enzymes in complex proteomes. These probes in turn are equipped with a reporter tag that allows capturing, visualization, enrichment, identification, and quantification of its targets either in vitro or in situ. THL possesses bactericidal activities, but its precise spectrum of molecular targets is poorly characterized. Here, we used THL analogs functionalized to enable Huisgen-base cycloaddition, commonly known as "click chemistry," to identify target proteins after enrichment from mycobacterial cell lysates obtained from different physiological conditions.
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Affiliation(s)
- Madhu Sudhan Ravindran
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore (NUS), Singapore, 117456, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore, 117456, Singapore.,Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Markus R Wenk
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore (NUS), Singapore, 117456, Singapore. .,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore, 117456, Singapore. .,Department of Biological Sciences, National University of Singapore (NUS), Singapore, 117456, Singapore. .,Swiss Tropical and Public Health Institute, University of Basel, 4051, Basel, Switzerland.
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Sharifzadeh S, Shirley JD, Carlson EE. Activity-Based Protein Profiling Methods to Study Bacteria: The Power of Small-Molecule Electrophiles. Curr Top Microbiol Immunol 2018; 420:23-48. [PMID: 30232601 DOI: 10.1007/82_2018_135] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
ABPP methods have been utilized for the last two decades as a means to investigate complex proteomes in all three domains of life. Extensive use in eukaryotes has provided a more fundamental understanding of the biological processes involved in numerous diseases and has driven drug discovery and treatment campaigns. However, the use of ABPP in prokaryotes has been less common, although it has gained more attention over the last decade. The urgent need for understanding bacteriophysiology and bacterial pathogenicity at a foundational level has never been more apparent, as the rise in antibiotic resistance has resulted in the inadequate and ineffective treatment of infections. This is not only a result of resistance to clinically used antibiotics, but also a lack of new drugs and equally as important, new drug targets. ABPP provides a means for which new, clinically relevant drug targets may be identified through gaining insight into biological processes. In this chapter, we place particular focus on the discussion of ABPP strategies that have been applied to study different classes of bacterial enzymes.
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Affiliation(s)
- Shabnam Sharifzadeh
- Department of Chemistry, University of Minnesota-Twin Cities, Minneapolis, MN, 55455, USA
| | - Joshua D Shirley
- Department of Medicinal Chemistry, University of Minnesota-Twin Cities, Minneapolis, MN, 55455, USA
| | - Erin E Carlson
- Department of Chemistry, University of Minnesota-Twin Cities, Minneapolis, MN, 55455, USA. .,Department of Medicinal Chemistry, University of Minnesota-Twin Cities, Minneapolis, MN, 55455, USA. .,Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota-Twin Cities, Minneapolis, MN, 55455, USA.
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Höper T, Mussotter F, Haase A, Luch A, Tralau T. Application of proteomics in the elucidation of chemical-mediated allergic contact dermatitis. Toxicol Res (Camb) 2017; 6:595-610. [PMID: 30090528 PMCID: PMC6062186 DOI: 10.1039/c7tx00058h] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 06/07/2017] [Indexed: 12/23/2022] Open
Abstract
Allergic contact dermatitis (ACD) is a widespread hypersensitivity reaction of the skin. The cellular mechanisms underlying its development are complex and involve close interaction of different cell types of the immune system. It is this very complexity which has long prevented straightforward replacement of the corresponding regulatory in vivo tests. Recent efforts have already resulted in the development of several in vitro testing alternatives that address key steps of ACD. Yet identification of suitable biomarkers is still a subject of intense research. Search strategies for the latter encompass transcriptomics, proteomics as well as metabolomics approaches. The scope of this review shall be the application and use of proteomics in the context of ACD. This includes highlighting relevant aspects of the molecular and cellular mechanisms underlying ACD, the exploitation of these mechanisms for testing and biomarkers (e.g., in the context of the OECD's adverse outcome pathway initiative) as well as an outlook on emerging proteome targets, for example during the allergen-induced activation of dendritic cells (DCs).
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Affiliation(s)
- Tessa Höper
- German Federal Institute for Risk Assessment , Department of Chemical and Product Safety , Max-Dohrn-Strasse 8-10 , 10589 Berlin , Germany .
| | - Franz Mussotter
- German Federal Institute for Risk Assessment , Department of Chemical and Product Safety , Max-Dohrn-Strasse 8-10 , 10589 Berlin , Germany .
| | - Andrea Haase
- German Federal Institute for Risk Assessment , Department of Chemical and Product Safety , Max-Dohrn-Strasse 8-10 , 10589 Berlin , Germany .
| | - Andreas Luch
- German Federal Institute for Risk Assessment , Department of Chemical and Product Safety , Max-Dohrn-Strasse 8-10 , 10589 Berlin , Germany .
| | - Tewes Tralau
- German Federal Institute for Risk Assessment , Department of Chemical and Product Safety , Max-Dohrn-Strasse 8-10 , 10589 Berlin , Germany .
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Liu J, Jiang T, Jiang F, Xu D, Wei L, Wang C, Chen Z, Zhang X, Li J. Comparative proteomic analysis of serum diagnosis patterns of sputum smear-positive pulmonary tuberculosis based on magnetic bead separation and mass spectrometry analysis. Int J Clin Exp Med 2015; 8:2077-2085. [PMID: 25932138 PMCID: PMC4402785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Accepted: 01/21/2015] [Indexed: 06/04/2023]
Abstract
A major challenge in pulmonary tuberculosis (TB) control is early and accurate diagnosis of sputum smear negative pulmonary TB (SSN-PTB). The patients with SSN-PTB have to wait for a longer period of time before receiving proper treatment than sputum smear positive pulmonary TB (SSP-PTB) patients due to delay in diagnosis. The purpose of this study is to discover potential serum protein biomarkers for SSN-PTB. Surface-enhanced laser desorption/ionization-time of flight mass spectrometry (SELDI-TOF MS) combined with weak cation exchange (WCX) magnetic beads was used to screen serum samples from SSN-PTB patients (N = 66), SSP-PTB patients (N = 49), and healthy volunteers (N = 80). The serum protein profiles were analyzed with Biomarker Wizard system. A classification model was established using Biomarker Pattern Software (BPS). Fifty-eight protein peaks were identified to exhibit significant differences between SSN-PTB, SSP-PTB and healthy control groups (P < 0.05), among which 6 peaks were found to be down-regulated, while 10 peaks were up-regulated gradually in the healthy control, SSN-PTB, and SSP-PTB groups. Twenty-three discriminating m/z peaks were detected between SSN-PTB patients and healthy controls (P < 0.01, Fold ≥ 1.5). The classification tree combined with three protein peaks (2747.0, 4480.0, and 9410.1 Da) could distinguish SSN-PTB patients from healthy controls with a sensitivity of 83.33% and a specificity of 82.50%. Early diagnosis of SSN-PTB disease is critical in order to reduce morbidity and mortality associated with TB. The study will help to clarify the role of differential proteins in the pathogenesis of TB.
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Affiliation(s)
- Jiyan Liu
- College of Life and Environmental Sciences, Hangzhou Normal UniversityHangzhou, P. R. China
| | - Tingting Jiang
- Institute of Cell Biology, Zhejiang UniversityHangzhou, P. R. China
| | - Feng Jiang
- Dongzhimen Hospital Affiliated to Beijing University of Chinese MedicineBeijing, P. R. China
| | - Dandan Xu
- Institute of Cell Biology, Zhejiang UniversityHangzhou, P. R. China
| | - Liliang Wei
- Department of Respiratory Medicine, The Sixth Hospital of ShaoxingShaoxing, P. R. China
| | - Chong Wang
- Institute of Cell Biology, Zhejiang UniversityHangzhou, P. R. China
| | - Zhongliang Chen
- Institute of Cell Biology, Zhejiang UniversityHangzhou, P. R. China
| | - Xing Zhang
- Institute of Cell Biology, Zhejiang UniversityHangzhou, P. R. China
| | - Jicheng Li
- Institute of Cell Biology, Zhejiang UniversityHangzhou, P. R. China
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Hanash S, Schliekelman M. Proteomic profiling of the tumor microenvironment: recent insights and the search for biomarkers. Genome Med 2014; 6:12. [PMID: 24713112 PMCID: PMC3978437 DOI: 10.1186/gm529] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Although gain of oncogene functions and loss of tumor suppressor functions are driving forces in tumor development, the tumor microenvironment, comprising the extracellular matrix, surrounding stroma, signaling molecules and infiltrating immune and other cell populations, is now also recognized as crucial to tumor development and metastasis. Many interactions at the tumor cell-environment interface occur at the protein level. Proteomic approaches are contributing to the definition of the protein constituents of the microenvironment and their sources, modifications, interactions and turnover, as well as providing information on how these features relate to tumor development and progression. Recently, proteomic studies have revealed how cancer cells modulate the microenvironment through their secreted proteins and how they can alter their protein constituents to adapt to the microenvironment. Moreover, the release of proteins from the microenvironment into the circulatory system has relevance for the development of blood-based cancer diagnostics. Here, we review how proteomic approaches are being applied to studies of the tumor microenvironment to decipher tumor-stroma interactions and to elucidate the role of host cells in the tumor microenvironment.
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Marshall RP, Simpson JK, Lukey PT. Strategies for biomarker discovery in fibrotic disease. Biochim Biophys Acta Mol Basis Dis 2013; 1832:1079-87. [PMID: 23376113 DOI: 10.1016/j.bbadis.2013.01.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2012] [Revised: 01/18/2013] [Accepted: 01/22/2013] [Indexed: 01/06/2023]
Abstract
The discovery and development of biomarkers for fibrotic diseases have potential utility in clinical decision-making as well as in pharmaceutical research and development. This review describes strategies for identifying diagnostic, prognostic and theranostic biomarkers. A range of technologies and platforms for biomarker discovery are highlighted, including several with specific relevance for fibrosis. Some challenges specific to fibrotic diseases are outlined including; benchmarking biomarkers against imperfect clinical measures of fibrosis, the complexity resulting from diverse aetiologies and target organs, and the availability of samples (including biopsy) from well-characterised patients with fibrotic disease. To overcome these challenges collaboration amongst clinical specialities as well as between academia and industry is essential. This article is part of a Special Issue entitled: Fibrosis: Translation of basic research to human disease.
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Affiliation(s)
- Richard P Marshall
- Fibrosis Discovery Performance Unit, GlaxoSmithKline R&D, GlaxoSmithKline Medicines Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, UK.
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