1
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Daly L, Byrne DP, Perkins S, Brownridge PJ, McDonnell E, Jones AR, Eyers PA, Eyers CE. Custom Workflow for the Confident Identification of Sulfotyrosine-Containing Peptides and Their Discrimination from Phosphopeptides. J Proteome Res 2023; 22:3754-3772. [PMID: 37939282 PMCID: PMC10696596 DOI: 10.1021/acs.jproteome.3c00425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 09/30/2023] [Accepted: 10/13/2023] [Indexed: 11/10/2023]
Abstract
Protein tyrosine sulfation (sY) is a post-translational modification (PTM) catalyzed by Golgi-resident tyrosyl protein sulfo transferases (TPSTs). Information on sY in humans is currently limited to ∼50 proteins, with only a handful having verified sites of sulfation. As such, the contribution of sulfation to the regulation of biological processes remains poorly defined. Mass spectrometry (MS)-based proteomics is the method of choice for PTM analysis but has yet to be applied for systematic investigation of the "sulfome", primarily due to issues associated with discrimination of sY-containing from phosphotyrosine (pY)-containing peptides. In this study, we developed an MS-based workflow for sY-peptide characterization, incorporating optimized Zr4+ immobilized metal-ion affinity chromatography (IMAC) and TiO2 enrichment strategies. Extensive characterization of a panel of sY- and pY-peptides using an array of fragmentation regimes (CID, HCD, EThcD, ETciD, UVPD) highlighted differences in the generation of site-determining product ions and allowed us to develop a strategy for differentiating sulfated peptides from nominally isobaric phosphopeptides based on low collision energy-induced neutral loss. Application of our "sulfomics" workflow to a HEK-293 cell extracellular secretome facilitated identification of 21 new sulfotyrosine-containing proteins, several of which we validate enzymatically, and reveals new interplay between enzymes relevant to both protein and glycan sulfation.
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Affiliation(s)
- Leonard
A. Daly
- Centre
for Proteome Research, Institute of Systems, Molecular & Integrative
Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, U.K.
- Department
of Biochemistry, Cell & Systems Biology, Institute of Systems,
Molecular & Integrative Biology, University
of Liverpool, Crown Street, Liverpool L69 7ZB, U.K.
| | - Dominic P. Byrne
- Department
of Biochemistry, Cell & Systems Biology, Institute of Systems,
Molecular & Integrative Biology, University
of Liverpool, Crown Street, Liverpool L69 7ZB, U.K.
| | - Simon Perkins
- Computational
Biology Facility, Institute of Systems, Molecular & Integrative
Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, U.K.
| | - Philip J. Brownridge
- Centre
for Proteome Research, Institute of Systems, Molecular & Integrative
Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, U.K.
| | - Euan McDonnell
- Department
of Biochemistry, Cell & Systems Biology, Institute of Systems,
Molecular & Integrative Biology, University
of Liverpool, Crown Street, Liverpool L69 7ZB, U.K.
- Computational
Biology Facility, Institute of Systems, Molecular & Integrative
Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, U.K.
| | - Andrew R. Jones
- Department
of Biochemistry, Cell & Systems Biology, Institute of Systems,
Molecular & Integrative Biology, University
of Liverpool, Crown Street, Liverpool L69 7ZB, U.K.
- Computational
Biology Facility, Institute of Systems, Molecular & Integrative
Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, U.K.
| | - Patrick A. Eyers
- Department
of Biochemistry, Cell & Systems Biology, Institute of Systems,
Molecular & Integrative Biology, University
of Liverpool, Crown Street, Liverpool L69 7ZB, U.K.
| | - Claire E. Eyers
- Centre
for Proteome Research, Institute of Systems, Molecular & Integrative
Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, U.K.
- Department
of Biochemistry, Cell & Systems Biology, Institute of Systems,
Molecular & Integrative Biology, University
of Liverpool, Crown Street, Liverpool L69 7ZB, U.K.
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2
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Daly LA, Clarke CJ, Po A, Oswald SO, Eyers CE. Considerations for defining +80 Da mass shifts in mass spectrometry-based proteomics: phosphorylation and beyond. Chem Commun (Camb) 2023; 59:11484-11499. [PMID: 37681662 PMCID: PMC10521633 DOI: 10.1039/d3cc02909c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 08/21/2023] [Indexed: 09/09/2023]
Abstract
Post-translational modifications (PTMs) are ubiquitous and key to regulating protein function. Understanding the dynamics of individual PTMs and their biological roles requires robust characterisation. Mass spectrometry (MS) is the method of choice for the identification and quantification of protein modifications. This article focusses on the MS-based analysis of those covalent modifications that induce a mass shift of +80 Da, notably phosphorylation and sulfation, given the challenges associated with their discrimination and pinpointing the sites of modification on a polypeptide chain. Phosphorylation in particular is highly abundant, dynamic and can occur on numerous residues to invoke specific functions, hence robust characterisation is crucial to understanding biological relevance. Showcasing our work in the context of other developments in the field, we highlight approaches for enrichment and site localisation of phosphorylated (canonical and non-canonical) and sulfated peptides, as well as modification analysis in the context of intact proteins (top down proteomics) to explore combinatorial roles. Finally, we discuss the application of native ion-mobility MS to explore the effect of these PTMs on protein structure and ligand binding.
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Affiliation(s)
- Leonard A Daly
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
| | - Christopher J Clarke
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
| | - Allen Po
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
| | - Sally O Oswald
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
| | - Claire E Eyers
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
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3
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Wu X, Liu YK, Iliuk AB, Tao WA. Mass spectrometry-based phosphoproteomics in clinical applications. Trends Analyt Chem 2023; 163:117066. [PMID: 37215489 PMCID: PMC10195102 DOI: 10.1016/j.trac.2023.117066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Protein phosphorylation is an essential post-translational modification that regulates many aspects of cellular physiology, and dysregulation of pivotal phosphorylation events is often responsible for disease onset and progression. Clinical analysis on disease-relevant phosphoproteins, while quite challenging, provides unique information for precision medicine and targeted therapy. Among various approaches, mass spectrometry (MS)-centered characterization features discovery-driven, high-throughput and in-depth identification of phosphorylation events. This review highlights advances in sample preparation and instrument in MS-based phosphoproteomics and recent clinical applications. We emphasize the preeminent data-independent acquisition method in MS as one of the most promising future directions and biofluid-derived extracellular vesicles as an intriguing source of the phosphoproteome for liquid biopsy.
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Affiliation(s)
- Xiaofeng Wu
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Yi-Kai Liu
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
| | - Anton B. Iliuk
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
- Tymora Analytical Operations, West Lafayette, IN, USA
| | - W. Andy Tao
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
- Tymora Analytical Operations, West Lafayette, IN, USA
- Center for Cancer Research, Purdue University, West Lafayette, IN, USA
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4
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Li J, Zhan X. Mass spectrometry analysis of phosphotyrosine-containing proteins. MASS SPECTROMETRY REVIEWS 2023. [PMID: 36789499 DOI: 10.1002/mas.21836] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 12/19/2022] [Accepted: 01/24/2023] [Indexed: 06/18/2023]
Abstract
Tyrosine phosphorylation is a crucial posttranslational modification that is involved in various aspects of cell biology and often has functions in cancers. It is necessary not only to identify the specific phosphorylation sites but also to quantify their phosphorylation levels under specific pathophysiological conditions. Because of its high sensitivity and accuracy, mass spectrometry (MS) has been widely used to identify endogenous and synthetic phosphotyrosine proteins/peptides across a range of biological systems. However, phosphotyrosine-containing proteins occur in extremely low abundance and they degrade easily, severely challenging the application of MS. This review highlights the advances in both quantitative analysis procedures and enrichment approaches to tyrosine phosphorylation before MS analysis and reviews the differences among phosphorylation, sulfation, and nitration of tyrosine residues in proteins. In-depth insights into tyrosine phosphorylation in a wide variety of biological systems will offer a deep understanding of how signal transduction regulates cellular physiology and the development of tyrosine phosphorylation-related drugs as cancer therapeutics.
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Affiliation(s)
- Jiajia Li
- Medical Science and Technology Innovation Center, Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, Shandong, Jinan, People's Republic of China
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Central South University, Changsha, Hunan, People's Republic of China
| | - Xianquan Zhan
- Medical Science and Technology Innovation Center, Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, Shandong, Jinan, People's Republic of China
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5
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Carrillo-Rodriguez P, Selheim F, Hernandez-Valladares M. Mass Spectrometry-Based Proteomics Workflows in Cancer Research: The Relevance of Choosing the Right Steps. Cancers (Basel) 2023; 15:cancers15020555. [PMID: 36672506 PMCID: PMC9856946 DOI: 10.3390/cancers15020555] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 01/12/2023] [Indexed: 01/19/2023] Open
Abstract
The qualitative and quantitative evaluation of proteome changes that condition cancer development can be achieved with liquid chromatography-mass spectrometry (LC-MS). LC-MS-based proteomics strategies are carried out according to predesigned workflows that comprise several steps such as sample selection, sample processing including labeling, MS acquisition methods, statistical treatment, and bioinformatics to understand the biological meaning of the findings and set predictive classifiers. As the choice of best options might not be straightforward, we herein review and assess past and current proteomics approaches for the discovery of new cancer biomarkers. Moreover, we review major bioinformatics tools for interpreting and visualizing proteomics results and suggest the most popular machine learning techniques for the selection of predictive biomarkers. Finally, we consider the approximation of proteomics strategies for clinical diagnosis and prognosis by discussing current barriers and proposals to circumvent them.
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Affiliation(s)
- Paula Carrillo-Rodriguez
- Proteomics Unit of University of Bergen (PROBE), University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway
- Vall d'Hebron Institute of Oncology (VHIO), 08035 Barcelona, Spain
| | - Frode Selheim
- Proteomics Unit of University of Bergen (PROBE), University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway
| | - Maria Hernandez-Valladares
- Proteomics Unit of University of Bergen (PROBE), University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway
- Department of Physical Chemistry, University of Granada, Avenida de la Fuente Nueva S/N, 18071 Granada, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, 18012 Granada, Spain
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6
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Mithoe SC, Menke FLH. Titanium Oxide-Based Phosphopeptide Enrichment from Arabidopsis Seedlings. Methods Mol Biol 2023; 2581:255-265. [PMID: 36413323 DOI: 10.1007/978-1-0716-2784-6_18] [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] [Indexed: 06/16/2023]
Abstract
Protein phosphorylation is one of the most widely studied posttranslational modifications, and its role in signal transduction has gained particular attention. The relatively low abundance of the phosphorylated form of proteins makes identification by mass spectrometry challenging in the absence of selective enrichment. Titanium oxide-based enrichment of phosphopeptides in the presence of acidic modifiers is highly selective and makes it technically possible to detect thousands of phosphopeptides in a single sample by liquid chromatography-mass spectrometry. In this chapter, we describe a detailed protocol for the selective enrichment of microsomal and cytosolic phosphopeptides from Arabidopsis seedlings. The resulting phosphopeptide fractions enable routine identification of several thousands of phosphopeptide spectra per sample by mass spectrometry.
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Affiliation(s)
| | - Frank L H Menke
- The Sainsbury Laboratory, Norwich Research Park, University of East Anglia, Norwich, UK.
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7
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Translational proteomics and phosphoproteomics: Tissue to extracellular vesicles. Adv Clin Chem 2022; 112:119-153. [PMID: 36642482 DOI: 10.1016/bs.acc.2022.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We are currently experiencing a rapidly developing era in terms of translational and clinical medical sciences. The relatively mature state of nucleic acid examination has significantly improved our understanding of disease mechanism and therapeutic potential of personalized treatment, but misses a large portion of phenotypic disease information. Proteins, in particular phosphorylation events that regulates many cellular functions, could provide real-time information for disease onset, progression and treatment efficacy. The technical advances in liquid chromatography and mass spectrometry have realized large-scale and unbiased proteome and phosphoproteome analyses with disease relevant samples such as tissues. However, tissue biopsy still has multiple shortcomings, such as invasiveness of sample collection, potential health risk for patients, difficulty in protein preservation and extreme heterogeneity. Recently, extracellular vesicles (EVs) have offered a great promise as a unique source of protein biomarkers for non-invasive liquid biopsy. Membranous EVs provide stable preservation of internal proteins and especially labile phosphoproteins, which is essential for effective routine biomarker detection. To aid efficient EV proteomic and phosphoproteomic analyses, recent developments showcase clinically-friendly EV techniques, facilitating diagnostic and therapeutic applications. Ultimately, we envision that with streamlined sample preparation from tissues and EVs proteomics and phosphoproteomics analysis will become routine in clinical settings.
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8
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King CD, Kapp KL, Arul AB, Choi MJ, Robinson RAS. Advancements in automation for plasma proteomics sample preparation. Mol Omics 2022; 18:828-839. [PMID: 36048090 PMCID: PMC9879274 DOI: 10.1039/d2mo00122e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Automation is necessary to increase sample processing throughput for large-scale clinical analyses. Replacement of manual pipettes with robotic liquid handler systems is especially helpful in processing blood-based samples, such as plasma and serum. These samples are very heterogenous, and protein expression can vary greatly from sample-to-sample, even for healthy controls. Detection of true biological changes requires that variation from sample preparation steps and downstream analytical detection methods, such as mass spectrometry, remains low. In this mini-review, we discuss plasma proteomics protocols and the benefits of automation towards enabling detection of low abundant proteins and providing low sample error and increased sample throughput. This discussion includes considerations for automation of major sample depletion and/or enrichment strategies for plasma toward mass spectrometry detection.
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Affiliation(s)
- Christina D King
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, USA
| | - Kathryn L Kapp
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, USA
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37232, USA
| | - Albert B Arul
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, USA
| | - Min Ji Choi
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, USA
| | - Renã A S Robinson
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, USA
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37232, USA
- Department of Neurology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, USA
- Vanderbilt Memory & Alzheimer's Center, Vanderbilt University Medical Center, Nashville, Tennessee 37212, USA
- Vanderbilt Brain Institute, Vanderbilt University, Nashville, Tennessee 37232, USA
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9
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Ino Y, Nishi M, Yamaoka Y, Miyakawa K, Jeremiah SS, Osada M, Kimura Y, Ryo A. Phosphopeptide enrichment using Phos-tag technology reveals functional phosphorylation of the nucleocapsid protein of SARS-CoV-2. J Proteomics 2022; 255:104501. [PMID: 35093569 PMCID: PMC8800104 DOI: 10.1016/j.jprot.2022.104501] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 01/19/2022] [Accepted: 01/23/2022] [Indexed: 11/28/2022]
Abstract
Phosphorylation of viral proteins serves as a regulatory mechanism during the intracellular life cycle of infected viruses. There is therefore a pressing need to develop a method to efficiently purify and enrich phosphopeptides derived from viral particles in biological samples. In this study, we utilized Phos-tag technology to analyze the functional phosphorylation of the nucleocapsid protein (N protein; NP) of severe respiratory syndrome coronavirus 2 (SARS-CoV-2). Viral particles were collected from culture supernatants of SARS-CoV-2-infected VeroE6/TMPRSS2 cells by ultracentrifugation, and phosphopeptides were purified by Phos-tag magnetic beads for LC-MS/MS analysis. Analysis revealed that NP was reproducibly phosphorylated at serine 79 (Ser79). Multiple sequence alignment and phylogenetic analysis showed that the Ser79 was a distinct phospho-acceptor site in SARS-CoV-2 but not in other beta-coronaviruses. We also found that the prolyl-isomerase Pin1 bound to the phosphorylated Ser79 in NP and positively regulated the production of viral particles. These results suggest that SARS-CoV-2 may have acquired the potent virus-host interaction during its evolution mediated by viral protein phosphorylation. Moreover, Phos-tag technology can provide a useful means for analyzing the functional phosphorylation of viral proteins. Significance In this study, we aimed to investigate the functional phosphorylation of SARS-CoV-2 NP. For this purpose, we used Phos-tag technology to purify and enrich virus-derived phosphopeptides with high selectivity and reproducibility. This method can be particularly useful in analyzing viral phosphopeptides from cell culture supernatants that often contain high concentrations of fetal bovine serum and supplements. We newly identified an NP phosphorylation site at Ser79, which is important for Pin1 binding. Furthermore, we showed that the interaction between Pin1 and phosphorylated NP could enhance viral replication in a cell culture model.
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Affiliation(s)
- Yoko Ino
- Advanced Medical Research Center, Yokohama City University, Fukuura 3-9, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan; Graduate School of Health Sciences, Gunma Paz University, Tonyamachi 1-7-1, Takasaki-shi, Gunma 370-0006, Japan
| | - Mayuko Nishi
- Department of Microbiology, School of Medicine, Yokohama City University, Fukuura 3-9, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan
| | - Yutaro Yamaoka
- Department of Microbiology, School of Medicine, Yokohama City University, Fukuura 3-9, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan; Life Science Laboratory, Technology and Development Division, Kanto Chemical Co., Inc., Suzukawa 21, Isehara-shi, Kanagawa 259-1146, Japan
| | - Kei Miyakawa
- Department of Microbiology, School of Medicine, Yokohama City University, Fukuura 3-9, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan
| | - Sundararaj Stanleyraj Jeremiah
- Department of Microbiology, School of Medicine, Yokohama City University, Fukuura 3-9, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan
| | - Makoto Osada
- Graduate School of Health Sciences, Gunma Paz University, Tonyamachi 1-7-1, Takasaki-shi, Gunma 370-0006, Japan
| | - Yayoi Kimura
- Advanced Medical Research Center, Yokohama City University, Fukuura 3-9, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan
| | - Akihide Ryo
- Advanced Medical Research Center, Yokohama City University, Fukuura 3-9, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan; Department of Microbiology, School of Medicine, Yokohama City University, Fukuura 3-9, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan.
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10
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Perron N, Tan B, Dufresne C, Chen S. Proteomics and phosphoproteomics of C3 to CAM transition in the common ice plant. Methods Enzymol 2022; 676:347-368. [DOI: 10.1016/bs.mie.2022.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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11
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Jiao F, Gao F, Liu Y, Fan Z, Xiang X, Xia C, Lv Y, Xie Y, Bai H, Zhang W, Qin W, Qian X. A facile "one-material" strategy for tandem enrichment of small extracellular vesicles phosphoproteome. Talanta 2021; 223:121776. [PMID: 33298282 DOI: 10.1016/j.talanta.2020.121776] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 10/09/2020] [Accepted: 10/12/2020] [Indexed: 01/08/2023]
Abstract
Small extracellular vesicles (SEVs), are cell-derived, membrane-enclosed nanometer-sized vesicles that play vital roles in many biological processes. Recent years, more and more evidences proved that small EVs have close relationship with many diseases such as cancers and Alzheimer's disease. The use of phosphoproteins in SEVs as potential biomarkers is a promising new choice for early diagnosis and prognosis of cancer. However, current techniques for SEVs isolation still facing many challenges, such as highly instrument dependent, time consuming and insufficient purity. Furthermore, complex enrichment procedures and low microgram amounts of proteins available from clinical sources largely limit the throughput and the coveage depth of SEVs phosphoproteome mapping. Here, we synthesized Ti4+-modified magnetic graphene-oxide composites (GFST) and developed a "one-material" strategy for facile and efficient phosphoproteome enrichment and identification in SEVs from human serum. By taking advantage of chelation and electrostatic interactions between metal ions and phosphate groups, GFST shows excellent performance in both SEVs isolation and phosphopeptide enrichment. Close to 85% recovery is achieved within a few minutes by simple incubation with GFST and magnetic separation. Proteome profiling of the isolated serum SEVs without phosphopeptide enrichment results in 515 proteins, which is approximately one-fold more than those otained by ultracentrifugation or coprecipitation kits. Further application of GFST in one-material-based enrichment led to identification of 859 phosphosites in 530 phosphoproteins. Kinase-substrate correlation analysis reveals enriched substrates of CAMK in serum SEVs phosphoproteome. Therefore, we expect that the low instrument dependency and the limited sample requirement of this new strategy may facilitate clinical investigations in SEV-based transportation of abnormal kinases and substrates for drug target discovery and cancer monitoring.
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Affiliation(s)
- Fenglong Jiao
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Fangyuan Gao
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Yuanyuan Liu
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Zhiya Fan
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Xiaochao Xiang
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Chaoshuang Xia
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Yayao Lv
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Yuping Xie
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Haihong Bai
- Phase I Clinical Trial Center, Capital Medical University Affiliated Beijing Shijitan Hospital University, Beijing, 100038, China
| | - Wanjun Zhang
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Weijie Qin
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing, 102206, China; College of Basic Medicine, Anhui Medical University, Hefei, 230032, China.
| | - Xiaohong Qian
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing, 102206, China
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12
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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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The challenge of detecting modifications on proteins. Essays Biochem 2020; 64:135-153. [PMID: 31957791 DOI: 10.1042/ebc20190055] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 12/17/2019] [Accepted: 12/19/2019] [Indexed: 12/16/2022]
Abstract
Post-translational modifications (PTMs) are integral to the regulation of protein function, characterising their role in this process is vital to understanding how cells work in both healthy and diseased states. Mass spectrometry (MS) facilitates the mass determination and sequencing of peptides, and thereby also the detection of site-specific PTMs. However, numerous challenges in this field continue to persist. The diverse chemical properties, low abundance, labile nature and instability of many PTMs, in combination with the more practical issues of compatibility with MS and bioinformatics challenges, contribute to the arduous nature of their analysis. In this review, we present an overview of the established MS-based approaches for analysing PTMs and the common complications associated with their investigation, including examples of specific challenges focusing on phosphorylation, lysine acetylation and redox modifications.
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14
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Abstract
Acetylation was initially discovered as a post-translational modification (PTM) on the unstructured, highly basic N-terminal tails of eukaryotic histones in the 1960s. Histone acetylation constitutes part of the "histone code", which regulates chromosome compaction and various DNA processes such as gene expression, recombination, and DNA replication. In bacteria, nucleoid-associated proteins (NAPs) are responsible these functions in that they organize and compact the chromosome and regulate some DNA processes. The highly conserved DNABII family of proteins are considered functional homologues of eukaryotic histones despite having no sequence or structural conservation. Within the past decade, a growing interest in Nε-lysine acetylation led to the discovery that hundreds of bacterial proteins are acetylated with diverse cellular functions, in direct contrast to the original thought that this was a rare phenomenon. Similarly, other previously undiscovered bacterial PTMs, like serine, threonine, and tyrosine phosphorylation, have also been characterized. In this review, the various PTMs that were discovered among DNABII family proteins, specifically histone-like protein (HU) orthologues, from large-scale proteomic studies are discussed. The functional significance of these modifications and the enzymes involved are also addressed. The discovery of novel PTMs on these proteins begs this question: is there a histone-like code in bacteria?
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Affiliation(s)
- Valerie J Carabetta
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, New Jersey 08103, United States
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15
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Hernandez-Valladares M, Bruserud Ø, Selheim F. The Implementation of Mass Spectrometry-Based Proteomics Workflows in Clinical Routines of Acute Myeloid Leukemia: Applicability and Perspectives. Int J Mol Sci 2020; 21:ijms21186830. [PMID: 32957646 PMCID: PMC7556012 DOI: 10.3390/ijms21186830] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 09/10/2020] [Accepted: 09/15/2020] [Indexed: 02/08/2023] Open
Abstract
With the current reproducibility of proteome preparation workflows along with the speed and sensitivity of the mass spectrometers, the transition of the mass spectrometry (MS)-based proteomics technology from biomarker discovery to clinical implementation is under appraisal in the biomedicine community. Therefore, this technology might be implemented soon to detect well-known biomarkers in cancers and other diseases. Acute myeloid leukemia (AML) is an aggressive heterogeneous malignancy that requires intensive treatment to cure the patient. Leukemia relapse is still a major challenge even for patients who have favorable genetic abnormalities. MS-based proteomics could be of great help to both describe the proteome changes of individual patients and identify biomarkers that might encourage specific treatments or clinical strategies. Herein, we will review the advances and availability of the MS-based proteomics strategies that could already be used in clinical proteomics. However, the heterogeneity of complex diseases as AML requires consensus to recognize AML biomarkers and to establish MS-based workflows that allow their unbiased identification and quantification. Although our literature review appears promising towards the utilization of MS-based proteomics in clinical AML in a near future, major efforts are required to validate AML biomarkers and agree on clinically approved workflows.
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MESH Headings
- Biomarkers, Tumor/analysis
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Computational Biology
- Humans
- Leukemia, Myeloid, Acute/diagnosis
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/therapy
- Mass Spectrometry/methods
- Prognosis
- Proteome/analysis
- Proteome/metabolism
- Proteomics/methods
- Robotics/instrumentation
- Robotics/methods
- Workflow
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Affiliation(s)
- Maria Hernandez-Valladares
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway
- The Proteomics Facility of the University of Bergen (PROBE), Department of Biomedicine, University of Bergen, 5009 Bergen, Norway
- Correspondence: (M.H.-V.); (Ø.B.); (F.S.); Tel.: +47-55586368 (M.H.-V.); +47-55972997 (Ø.B.); +47-55586368 (F.S.)
| | - Øystein Bruserud
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway
- Correspondence: (M.H.-V.); (Ø.B.); (F.S.); Tel.: +47-55586368 (M.H.-V.); +47-55972997 (Ø.B.); +47-55586368 (F.S.)
| | - Frode Selheim
- The Proteomics Facility of the University of Bergen (PROBE), Department of Biomedicine, University of Bergen, 5009 Bergen, Norway
- The Department of Biomedicine, University of Bergen, 5009 Bergen, Norway
- Correspondence: (M.H.-V.); (Ø.B.); (F.S.); Tel.: +47-55586368 (M.H.-V.); +47-55972997 (Ø.B.); +47-55586368 (F.S.)
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16
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Rathore D, Nita-Lazar A. Phosphoproteome Analysis in Immune Cell Signaling. CURRENT PROTOCOLS IN IMMUNOLOGY 2020; 130:e105. [PMID: 32936995 PMCID: PMC10961162 DOI: 10.1002/cpim.105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Immune cell signaling is largely regulated by protein phosphorylation. Stimulation of toll-like receptors (TLRs) by pathogen-associated ligands drives the cascade of immune response, which can be influenced by differences in phosphoprotein abundance. Therefore, the analysis of phosphorylation signatures at a global level is central to understanding the complex and integrated signaling in macrophages upon pathogen attack. Here, we describe a mass spectrometry-based approach to identify and quantify phosphoproteome changes in response to the stimulation of TLR2, TLR4, and TLR7 with immune-response inducing ligands in cultured immune cells. This review will focus on the TLR stimulation of mouse macrophages as an example; however, the technique is applicable to any immortalized immune cell and any soluble stimuli. The methodology includes protocols for metabolic labeling of immune cells (stable isotope labeling of amino acids in cell culture, i.e., SILAC); ligand-initiated stimulation of immune receptors followed by cell lysis; in-solution trypsin digestion of proteins and enrichment of the resulting peptide mix for collecting phosphopeptides, which are then analyzed by high-resolution LC-MS/MS (liquid-chromatography tandem mass spectrometry). © 2020 Wiley Periodicals LLC. Basic Protocol 1: SILAC labeling of mouse macrophages Basic Protocol 2: Stimulation, cell lysis and Western Blotting Basic Protocol 3: Trypsin digestion, fractionation and phosphopeptide enrichment Basic Protocol 4: Quantitative mass spectrometry Alternate Protocol: Culturing SILAC-labeled cells from frozen mouse macrophages cells.
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Affiliation(s)
- Deepali Rathore
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Aleksandra Nita-Lazar
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
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17
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Bonne Køhler J, Jers C, Senissar M, Shi L, Derouiche A, Mijakovic I. Importance of protein Ser/Thr/Tyr phosphorylation for bacterial pathogenesis. FEBS Lett 2020; 594:2339-2369. [PMID: 32337704 DOI: 10.1002/1873-3468.13797] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 04/16/2020] [Accepted: 04/20/2020] [Indexed: 12/13/2022]
Abstract
Protein phosphorylation regulates a large variety of biological processes in all living cells. In pathogenic bacteria, the study of serine, threonine, and tyrosine (Ser/Thr/Tyr) phosphorylation has shed light on the course of infectious diseases, from adherence to host cells to pathogen virulence, replication, and persistence. Mass spectrometry (MS)-based phosphoproteomics has provided global maps of Ser/Thr/Tyr phosphosites in bacterial pathogens. Despite recent developments, a quantitative and dynamic view of phosphorylation events that occur during bacterial pathogenesis is currently lacking. Temporal, spatial, and subpopulation resolution of phosphorylation data is required to identify key regulatory nodes underlying bacterial pathogenesis. Herein, we discuss how technological improvements in sample handling, MS instrumentation, data processing, and machine learning should improve bacterial phosphoproteomic datasets and the information extracted from them. Such information is expected to significantly extend the current knowledge of Ser/Thr/Tyr phosphorylation in pathogenic bacteria and should ultimately contribute to the design of novel strategies to combat bacterial infections.
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Affiliation(s)
- Julie Bonne Køhler
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Carsten Jers
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Mériem Senissar
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Lei Shi
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Abderahmane Derouiche
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Ivan Mijakovic
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.,Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
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18
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Qiu W, Evans CA, Landels A, Pham TK, Wright PC. Phosphopeptide enrichment for phosphoproteomic analysis - A tutorial and review of novel materials. Anal Chim Acta 2020; 1129:158-180. [PMID: 32891386 DOI: 10.1016/j.aca.2020.04.053] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 04/23/2020] [Accepted: 04/24/2020] [Indexed: 12/12/2022]
Abstract
Significant technical advancements in phosphopeptide enrichment have enabled the identification of thousands of p-peptides (mono and multiply phosphorylated) in a single experiment. However, it is still not possible to enrich all p-peptide species in a single step. A range of new techniques and materials has been developed, with the potential to provide a step-change in phosphopeptide enrichment. The first half of this review contains a tutorial for new potential phosphoproteomic researchers; discussing the key steps of a typical phosphoproteomic experiment used to investigate canonical phosphorylation sites (serine, threonine and tyrosine). The latter half then show-cases the latest developments in p-peptide enrichment including: i) Strategies to mitigate non-specific binding in immobilized metal ion affinity chromatography and metal oxide affinity chromatography protocols; ii) Techniques to separate multiply phosphorylated peptides from monophosphorylated peptides (including canonical from non-canonical phosphorylated peptides), or to simultaneously co-enrich other post-translational modifications; iii) New hybrid materials and methods directed towards enhanced selectivity and efficiency of metal-based enrichment; iv) Novel materials that hold promise for enhanced phosphotyrosine enrichment. A combination of well-understood techniques and materials is much more effective than any technique in isolation; but the field of phosphoproteomics currently requires benchmarking of novel materials against current methodologies to fully evaluate their utility in peptide based proteoform analysis.
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Affiliation(s)
- Wen Qiu
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, 310058, Hangzhou, China
| | - Caroline A Evans
- ChELSI Institute, Department of Chemical and Biological Engineering, The University of Sheffield, Mappin Street, Sheffield, S1 3JD, United Kingdom
| | - Andrew Landels
- ChELSI Institute, Department of Chemical and Biological Engineering, The University of Sheffield, Mappin Street, Sheffield, S1 3JD, United Kingdom
| | - Trong Khoa Pham
- ChELSI Institute, Department of Chemical and Biological Engineering, The University of Sheffield, Mappin Street, Sheffield, S1 3JD, United Kingdom
| | - Phillip C Wright
- School of Engineering, Faculty of Science, Agriculture and Engineering, Newcastle University, Newcastle Upon Tyne, NE1 7RU, United Kingdom.
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19
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Hentschker C, Maaß S, Junker S, Hecker M, Hammerschmidt S, Otto A, Becher D. Comprehensive Spectral Library from the Pathogenic Bacterium Streptococcus pneumoniae with Focus on Phosphoproteins. J Proteome Res 2020; 19:1435-1446. [DOI: 10.1021/acs.jproteome.9b00615] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Christian Hentschker
- Department of Microbial Proteomics, Institute of Microbiology; University of Greifswald, Felix-Hausdorff-Str. 8, 17489 Greifswald, Germany
| | - Sandra Maaß
- Department of Microbial Proteomics, Institute of Microbiology; University of Greifswald, Felix-Hausdorff-Str. 8, 17489 Greifswald, Germany
| | - Sabryna Junker
- Department of Microbial Proteomics, Institute of Microbiology; University of Greifswald, Felix-Hausdorff-Str. 8, 17489 Greifswald, Germany
| | - Michael Hecker
- Department of Microbial Physiology and Molecular Biology, Institute of Microbiology; University of Greifswald, Felix-Hausdorff-Str. 8, 17489 Greifswald, Germany
| | - Sven Hammerschmidt
- Department of Molecular Genetics and Infection Biology, Interfaculty Institute for Genetics and Functional Genomics, University of Greifswald, Felix-Hausdorff-Str. 8, 17489 Greifswald, Germany
| | - Andreas Otto
- Department of Microbial Proteomics, Institute of Microbiology; University of Greifswald, Felix-Hausdorff-Str. 8, 17489 Greifswald, Germany
| | - Dörte Becher
- Department of Microbial Proteomics, Institute of Microbiology; University of Greifswald, Felix-Hausdorff-Str. 8, 17489 Greifswald, Germany
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20
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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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21
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Goals and Challenges in Bacterial Phosphoproteomics. Int J Mol Sci 2019; 20:ijms20225678. [PMID: 31766156 PMCID: PMC6888350 DOI: 10.3390/ijms20225678] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 11/04/2019] [Accepted: 11/12/2019] [Indexed: 12/21/2022] Open
Abstract
Reversible protein phosphorylation at serine, threonine and tyrosine is a well-known dynamic post-translational modification with stunning regulatory and signalling functions in eukaryotes. Shotgun phosphoproteomic analyses revealed that this post-translational modification is dramatically lower in bacteria than in eukaryotes. However, Ser/Thr/Tyr phosphorylation is present in all analysed bacteria (24 eubacteria and 1 archaea). It affects central processes, such as primary and secondary metabolism development, sporulation, pathogenicity, virulence or antibiotic resistance. Twenty-nine phosphoprotein orthologues were systematically identified in bacteria: ribosomal proteins, enzymes from glycolysis and gluconeogenesis, elongation factors, cell division proteins, RNA polymerases, ATP synthases and enzymes from the citrate cycle. While Ser/Thr/Tyr phosphorylation exists in bacteria, there is a consensus that histidine phosphorylation is the most abundant protein phosphorylation in prokaryotes. Unfortunately, histidine shotgun phosphorproteomics is not possible due to the reduced phosphohistidine half-life under the acidic pH conditions used in standard LC-MS/MS analysis. However, considering the fast and continuous advances in LC-MS/MS-based phosphoproteomic methodologies, it is expected that further innovations will allow for the study of His phosphoproteomes and a better coverage of bacterial phosphoproteomes. The characterisation of the biological role of bacterial Ser/Thr/Tyr and His phosphorylations might revolutionise our understanding of prokaryotic physiology.
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22
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Pieroni L, Iavarone F, Olianas A, Greco V, Desiderio C, Martelli C, Manconi B, Sanna MT, Messana I, Castagnola M, Cabras T. Enrichments of post-translational modifications in proteomic studies. J Sep Sci 2019; 43:313-336. [PMID: 31631532 DOI: 10.1002/jssc.201900804] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 09/23/2019] [Accepted: 10/17/2019] [Indexed: 12/14/2022]
Abstract
More than 300 different protein post-translational modifications are currently known, but only a few have been extensively investigated because modified proteoforms are commonly present in sub-stoichiometry amount. For this reason, improvement of specific enrichment techniques is particularly useful for the proteomic characterization of post-translationally modified proteins. Enrichment proteomic strategies could help the researcher in the challenging issue to decipher the complex molecular cross-talk existing between the different factors influencing the cellular pathways. In this review the state of art of the platforms applied for the enrichment of specific and most common post-translational modifications, such as glycosylation and glycation, phosphorylation, sulfation, redox modifications (i.e. sulfydration and nitrosylation), methylation, acetylation, and ubiquitinylation, are described. Enrichments strategies applied to characterize less studied post-translational modifications are also briefly discussed.
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Affiliation(s)
- Luisa Pieroni
- Laboratorio di Proteomica e Metabolomica, Centro Europeo di Ricerca sul Cervello, IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Federica Iavarone
- Istituto di Biochimica e Biochimica Clinica, Facoltà di Medicina, Università Cattolica del Sacro Cuore, Rome, Italy.,IRCCS Fondazione Policlinico Universitario Agostino Gemelli, Rome, Italy
| | - Alessandra Olianas
- Dipartimento di Scienze della Vita e dell'Ambiente, Università di Cagliari, Cagliari, Italy
| | - Viviana Greco
- Istituto di Biochimica e Biochimica Clinica, Facoltà di Medicina, Università Cattolica del Sacro Cuore, Rome, Italy.,IRCCS Fondazione Policlinico Universitario Agostino Gemelli, Rome, Italy
| | - Claudia Desiderio
- Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche, Rome, Italy
| | - Claudia Martelli
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Barbara Manconi
- Dipartimento di Scienze della Vita e dell'Ambiente, Università di Cagliari, Cagliari, Italy
| | - Maria Teresa Sanna
- Dipartimento di Scienze della Vita e dell'Ambiente, Università di Cagliari, Cagliari, Italy
| | - Irene Messana
- Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche, Rome, Italy
| | - Massimo Castagnola
- Laboratorio di Proteomica e Metabolomica, Centro Europeo di Ricerca sul Cervello, IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Tiziana Cabras
- Dipartimento di Scienze della Vita e dell'Ambiente, Università di Cagliari, Cagliari, Italy
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23
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Kreher U, Spiccia L, Hearn MTW. Interactions between an amphipathic di-histidine peptide and a metal affinity chromatographic resin derived from a bis(tacn)butane chelating ligand. J Sep Sci 2019; 42:3631-3639. [PMID: 31651081 DOI: 10.1002/jssc.201900908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 10/04/2019] [Accepted: 10/04/2019] [Indexed: 11/06/2022]
Abstract
The interactive behavior of an amphipathic peptide with the Cu2+ , Ni2+ , and Zn2+ complexes of 1,4-bis(triazacyclonon-1-yl)butane), bis(tacn)but , immobilized onto Sepharose CL-4B, has been investigated. The effects of incubation time, as well as the incubation buffer pH and ionic strength, have been examined. The binding data have been interrogated using Langmuir, Langmuir-Freundlich, bi-Langmuir, and Temkin isothermal models and Scatchard plots. These results confirm that this amphipathic peptide binds with relatively high capacities to the immobilized Cu2+ - and Ni2+ -1,4-bis(triazacyclonon-1-yl)butane)-Sepharose CL-4B sorbents via at least two discrete sites. However, the corresponding immobilized Zn2+ -sorbent had low binding capacity. Moreover, the magnitude of the binding capacities of these sorbents was dependent on the pH and ionic strength of the incubation buffer. These results are relevant to the isolation of E. coli expressed recombinant proteins that incorporate this and related amphipathic peptide tags, containing two or more histidine residues, located at the N- or C-terminus of the recombinant protein, and the co-purification of low abundance host cell proteins of diverse structure, by immobilized metal ion affinity chromatographic methods.
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Affiliation(s)
- Ute Kreher
- Centre for Green Chemistry, School of Chemistry, Monash University, Clayton, Australia
| | - Leone Spiccia
- Centre for Green Chemistry, School of Chemistry, Monash University, Clayton, Australia
| | - Milton T W Hearn
- Centre for Green Chemistry, School of Chemistry, Monash University, Clayton, Australia
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24
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Huang J, Dong J, Shi X, Chen Z, Cui Y, Liu X, Ye M, Li L. Dual-Functional Titanium(IV) Immobilized Metal Affinity Chromatography Approach for Enabling Large-Scale Profiling of Protein Mannose-6-Phosphate Glycosylation and Revealing Its Predominant Substrates. Anal Chem 2019; 91:11589-11597. [PMID: 31398006 PMCID: PMC7293878 DOI: 10.1021/acs.analchem.9b01698] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Mannose-6-phosphate (M6P) glycosylation is an important post-translational modification (PTM) and plays a crucial role in transferring lysosomal hydrolases to lysosome, and is involved in several other biological processes. Aberrant M6P modifications have been implicated in lysosomal storage diseases and numerous other disorders including Alzheimer's disease and cancer. Research on profiling of intact M6P glycopeptides remains challenging due to its extremely low stoichiometry. Here we propose a dual-mode affinity approach to enrich M6P glycopeptides by dual-functional titanium(IV) immobilized metal affinity chromatography [Ti(IV)-IMAC] materials. In combination with state-of-the-art mass spectrometry and database search engine, we profiled 237 intact M6P glycopeptides corresponding to 81 M6P glycoproteins in five types of tissues in mouse, representing the first large-scale profiling of M6P glycosylation in mouse samples. The analysis of M6P glycoforms revealed the predominant glycan substrates of this PTM. Gene ontology analysis showed that overrepresented M6P glycoproteins were lysosomal-associated proteins. However, there were still substantial M6P glycoproteins that possessed different subcellular locations and molecular functions. Deep mining of their roles implicated in lysosomal and nonlysosomal function can provide new insights into functional roles of this important yet poorly studied modification.
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Affiliation(s)
- Junfeng Huang
- School of Pharmacy, University of Wisconsin, Madison, WI 53705, USA
| | - Jing Dong
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, China
| | - Xudong Shi
- Department of Surgery, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Zhengwei Chen
- Department of Chemistry, University of Wisconsin, Madison, WI 53705, USA
| | - Yusi Cui
- Department of Chemistry, University of Wisconsin, Madison, WI 53705, USA
| | - Xiaoyan Liu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, China
| | - Mingliang Ye
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, China
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin, Madison, WI 53705, USA
- Department of Chemistry, University of Wisconsin, Madison, WI 53705, USA
- School of Life Sciences, Tianjin University, Tianjin 300072, China
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25
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Gil J, Betancourt LH, Pla I, Sanchez A, Appelqvist R, Miliotis T, Kuras M, Oskolas H, Kim Y, Horvath Z, Eriksson J, Berge E, Burestedt E, Jönsson G, Baldetorp B, Ingvar C, Olsson H, Lundgren L, Horvatovich P, Murillo JR, Sugihara Y, Welinder C, Wieslander E, Lee B, Lindberg H, Pawłowski K, Kwon HJ, Doma V, Timar J, Karpati S, Szasz AM, Németh IB, Nishimura T, Corthals G, Rezeli M, Knudsen B, Malm J, Marko-Varga G. Clinical protein science in translational medicine targeting malignant melanoma. Cell Biol Toxicol 2019; 35:293-332. [PMID: 30900145 PMCID: PMC6757020 DOI: 10.1007/s10565-019-09468-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 02/13/2019] [Indexed: 02/06/2023]
Abstract
Melanoma of the skin is the sixth most common type of cancer in Europe and accounts for 3.4% of all diagnosed cancers. More alarming is the degree of recurrence that occurs with approximately 20% of patients lethally relapsing following treatment. Malignant melanoma is a highly aggressive skin cancer and metastases rapidly extend to the regional lymph nodes (stage 3) and to distal organs (stage 4). Targeted oncotherapy is one of the standard treatment for progressive stage 4 melanoma, and BRAF inhibitors (e.g. vemurafenib, dabrafenib) combined with MEK inhibitor (e.g. trametinib) can effectively counter BRAFV600E-mutated melanomas. Compared to conventional chemotherapy, targeted BRAFV600E inhibition achieves a significantly higher response rate. After a period of cancer control, however, most responsive patients develop resistance to the therapy and lethal progression. The many underlying factors potentially causing resistance to BRAF inhibitors have been extensively studied. Nevertheless, the remaining unsolved clinical questions necessitate alternative research approaches to address the molecular mechanisms underlying metastatic and treatment-resistant melanoma. In broader terms, proteomics can address clinical questions far beyond the reach of genomics, by measuring, i.e. the relative abundance of protein products, post-translational modifications (PTMs), protein localisation, turnover, protein interactions and protein function. More specifically, proteomic analysis of body fluids and tissues in a given medical and clinical setting can aid in the identification of cancer biomarkers and novel therapeutic targets. Achieving this goal requires the development of a robust and reproducible clinical proteomic platform that encompasses automated biobanking of patient samples, tissue sectioning and histological examination, efficient protein extraction, enzymatic digestion, mass spectrometry-based quantitative protein analysis by label-free or labelling technologies and/or enrichment of peptides with specific PTMs. By combining data from, e.g. phosphoproteomics and acetylomics, the protein expression profiles of different melanoma stages can provide a solid framework for understanding the biology and progression of the disease. When complemented by proteogenomics, customised protein sequence databases generated from patient-specific genomic and transcriptomic data aid in interpreting clinical proteomic biomarker data to provide a deeper and more comprehensive molecular characterisation of cellular functions underlying disease progression. In parallel to a streamlined, patient-centric, clinical proteomic pipeline, mass spectrometry-based imaging can aid in interrogating the spatial distribution of drugs and drug metabolites within tissues at single-cell resolution. These developments are an important advancement in studying drug action and efficacy in vivo and will aid in the development of more effective and safer strategies for the treatment of melanoma. A collaborative effort of gargantuan proportions between academia and healthcare professionals has led to the initiation, establishment and development of a cutting-edge cancer research centre with a specialisation in melanoma and lung cancer. The primary research focus of the European Cancer Moonshot Lund Center is to understand the impact that drugs have on cancer at an individualised and personalised level. Simultaneously, the centre increases awareness of the relentless battle against cancer and attracts global interest in the exceptional research performed at the centre.
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Affiliation(s)
- Jeovanis Gil
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden.
| | - Lazaro Hiram Betancourt
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden.
| | - Indira Pla
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
- Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Skåne University Hospital Malmö, 205 02, Malmö, Sweden
| | - Aniel Sanchez
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
- Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Skåne University Hospital Malmö, 205 02, Malmö, Sweden
| | - Roger Appelqvist
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Tasso Miliotis
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
- Translational Science, Cardiovascular Renal and Metabolism, IMED Biotech Unit, AstraZeneca, Gothenburg, Sweden
| | - Magdalena Kuras
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Henriette Oskolas
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Yonghyo Kim
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Zsolt Horvath
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Jonatan Eriksson
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Ethan Berge
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Elisabeth Burestedt
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Göran Jönsson
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85, Lund, Sweden
| | - Bo Baldetorp
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85, Lund, Sweden
| | - Christian Ingvar
- Department of Surgery, Clinical Sciences, Lund University, SUS, Lund, Sweden
| | - Håkan Olsson
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85, Lund, Sweden
| | - Lotta Lundgren
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85, Lund, Sweden
- Department of Haematology, Oncology and Radiation Physics, Skåne University Hospital, Lund, Sweden
| | - Peter Horvatovich
- Department of Analytical Biochemistry, Faculty of Science and Engineering, University of Groningen, Groningen, The Netherlands
| | - Jimmy Rodriguez Murillo
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Yutaka Sugihara
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Charlotte Welinder
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85, Lund, Sweden
| | - Elisabet Wieslander
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85, Lund, Sweden
| | - Boram Lee
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Henrik Lindberg
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Krzysztof Pawłowski
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
- Department of Experimental Design and Bioinformatics, Faculty of Agriculture and Biology, Warsaw University of Life Sciences, Warsaw, Poland
| | - Ho Jeong Kwon
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
- Chemical Genomics Global Research Lab, Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Viktoria Doma
- Second Department of Pathology, Semmelweis University, Budapest, Hungary
| | - Jozsef Timar
- Second Department of Pathology, Semmelweis University, Budapest, Hungary
| | - Sarolta Karpati
- Department of Dermatology, Semmelweis University, Budapest, Hungary
| | - A Marcell Szasz
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, 221 85, Lund, Sweden
- Cancer Center, Semmelweis University, Budapest, 1083, Hungary
- MTA-TTK Momentum Oncology Biomarker Research Group, Hungarian Academy of Sciences, Budapest, 1117, Hungary
| | - István Balázs Németh
- Department of Dermatology and Allergology, University of Szeged, Szeged, H-6720, Hungary
| | - Toshihide Nishimura
- Clinical Translational Medicine Informatics, St. Marianna University School of Medicine, Kawasaki, Kanagawa, Japan
- Department of Surgery, Tokyo Medical University, 6-7-1 Nishishinjiku Shinjiku-ku, Tokyo, Japan
| | - Garry Corthals
- Van't Hoff Institute of Molecular Sciences, 1090 GS, Amsterdam, The Netherlands
| | - Melinda Rezeli
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
| | - Beatrice Knudsen
- Biomedical Sciences and Pathology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Johan Malm
- Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Skåne University Hospital Malmö, 205 02, Malmö, Sweden
| | - György Marko-Varga
- Clinical Protein Science & Imaging, Biomedical Centre, Department of Biomedical Engineering, Lund University, BMC D13, 221 84, Lund, Sweden
- Chemical Genomics Global Research Lab, Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
- Department of Surgery, Tokyo Medical University, 6-7-1 Nishishinjiku Shinjiku-ku, Tokyo, Japan
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Chronic shisha exposure alters phosphoproteome of oral keratinocytes. J Cell Commun Signal 2019; 13:281-289. [PMID: 31321732 DOI: 10.1007/s12079-019-00528-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Accepted: 07/08/2019] [Indexed: 12/31/2022] Open
Abstract
Shisha smoking has been epidemiologically linked to oral cancer. However, few studies have investigated the pathobiology of shisha-induced cellular transformation. We studied the effects of chronic shisha exposure (8 months) in an in vitro model using immortalized, non-neoplastic oral keratinocytes (OKF6/TERT1). Quantitative proteomic and phosphoproteomic analyses were performed on OKF6/TERT1 cells treated with shisha extract for a period of 8 months. Pathway analysis was carried out to identify significantly enriched biological processes in shisha-treated cells. Chronic shisha exposure resulted in increased cell scattering phenomenon in OKF6/TERT1 cells. Data analysis revealed differential phosphorylation of 164 peptides (fold change ≥1.5, p ≤ 0.0.5) corresponding to 136 proteins. Proteins associated with mTORC1 and EIF4F complexes involved in initiating protein translation were seen to be enriched upon shisha treatment. Network analysis also highlighted downregulation of proteins involved in Type I interferon signaling in shisha-treated cells. Quantitative phosphoproteomic approach elucidated global perturbations to the molecular milieu of oral keratinocytes upon shisha exposure. Further studies are needed to validate putative targets in oral cancer patients with shisha smoking history.
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27
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Metal–organic framework-based affinity materials in proteomics. Anal Bioanal Chem 2019; 411:1745-1759. [DOI: 10.1007/s00216-019-01610-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 12/31/2018] [Accepted: 01/14/2019] [Indexed: 01/17/2023]
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Automated phosphopeptide enrichment from minute quantities of frozen malignant melanoma tissue. PLoS One 2018; 13:e0208562. [PMID: 30532160 PMCID: PMC6287822 DOI: 10.1371/journal.pone.0208562] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 11/19/2018] [Indexed: 11/19/2022] Open
Abstract
To acquire a deeper understanding of malignant melanoma (MM), it is essential to study the proteome of patient tissues. In particular, phosphoproteomics of MM has become of significant importance because of the central role that phosphorylation plays in the development of MM. Investigating clinical samples, however, is an extremely challenging task as there is usually only very limited quantities of material available to perform targeted enrichment approaches. Here, an automated phosphopeptide enrichment protocol using the AssayMap Bravo platform was applied to MM tissues and assessed for performance. The strategy proved to be highly-sensitive, less prone to variability, less laborious than existing techniques and adequate for starting quantities at the microgram level. An Fe(III)-NTA-IMAC-based enrichment workflow was applied to a dilution series of MM tissue lysates. The workflow was efficient in terms of sensitivity, reproducibility and phosphosite localization; and from only 12.5 μg of sample, more than 1,000 phosphopeptides were identified. In addition, from 60 μg of protein material the number of identified phosphoproteins from individual MM samples was comparable to previous reports that used extensive fractionation methods. Our data set included key pathways that are involved in MM progression; such as MAPK, melanocyte development and integrin signaling. Moreover, tissue-specific immunological proteins were identified, that have not been previously observed in the proteome of MM-derived cell lines. In conclusion, this workflow is suitable to study large cohorts of clinical samples that demand automatic and careful handling.
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29
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Núñez C, Chantada-Vázquez MDP, Bravo SB, Vázquez-Estévez S. Novel functionalized nanomaterials for the effective enrichment of proteins and peptides with post-translational modifications. J Proteomics 2018; 181:170-189. [DOI: 10.1016/j.jprot.2018.04.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 04/02/2018] [Accepted: 04/09/2018] [Indexed: 02/07/2023]
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30
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Lietz CB, Toneff T, Mosier C, Podvin S, O'Donoghue AJ, Hook V. Phosphopeptidomics Reveals Differential Phosphorylation States and Novel SxE Phosphosite Motifs of Neuropeptides in Dense Core Secretory Vesicles. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:935-947. [PMID: 29556927 PMCID: PMC5943185 DOI: 10.1007/s13361-018-1915-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 02/07/2018] [Accepted: 02/08/2018] [Indexed: 05/23/2023]
Abstract
Neuropeptides are vital for cell-cell communication and function in the regulation of the nervous and endocrine systems. They are generated by post-translational modification (PTM) steps resulting in small active peptides generated from prohormone precursors. Phosphorylation is a significant PTM for the bioactivity of neuropeptides. From the known diversity of distinct neuropeptide functions, it is hypothesized that the extent of phosphorylation varies among different neuropeptides. To assess this hypothesis, neuropeptide-containing dense core secretory vesicles from bovine adrenal medullary chromaffin cells were subjected to global phosphopeptidomics analyses by liquid chromatography (LC)-mass spectrometry (MS/MS). Phosphopeptides were identified directly by LC-MS/MS and indirectly by phosphatase treatment followed by LC-MS/MS. The data identified numerous phosphorylated peptides derived from neuropeptide precursors such as chromogranins, secretogranins, proenkephalin and pro-NPY. Phosphosite occupancies were observed at high and low levels among identified peptides and many of the high occupancy phosphopeptides represent prohormone-derived peptides with currently unknown bioactivities. Peptide sequence analyses demonstrated SxE as the most prevalent phosphorylation site motif, corresponding to phosphorylation sites of the Fam20C protein kinase known to be present in the secretory pathway. The range of high to low phosphosite occupancies for neuropeptides demonstrates cellular regulation of neuropeptide phosphorylation. Graphical Abstract ᅟ.
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Affiliation(s)
- Christopher B Lietz
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr. MC0719, La Jolla, CA, 92093-0719, USA
| | - Thomas Toneff
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr. MC0719, La Jolla, CA, 92093-0719, USA
| | - Charles Mosier
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr. MC0719, La Jolla, CA, 92093-0719, USA
| | - Sonia Podvin
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr. MC0719, La Jolla, CA, 92093-0719, USA
| | - Anthony J O'Donoghue
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr. MC0719, La Jolla, CA, 92093-0719, USA
| | - Vivian Hook
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr. MC0719, La Jolla, CA, 92093-0719, USA.
- Department of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA, 92093, USA.
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31
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Hernandez-Valladares M, Vaudel M, Selheim F, Berven F, Bruserud Ø. Proteogenomics approaches for studying cancer biology and their potential in the identification of acute myeloid leukemia biomarkers. Expert Rev Proteomics 2017; 14:649-663. [DOI: 10.1080/14789450.2017.1352474] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Maria Hernandez-Valladares
- Department of Clinical Science, Faculty of Medicine and Dentistry, University of Bergen, Bergen, Norway
- Proteomics Unit, Department of Biomedicine, Faculty of Medicine and Dentistry, University of Bergen, Bergen, Norway
| | - Marc Vaudel
- KG Jebsen Center for Diabetes Research, Department of Clinical Science, Faculty of Medicine and Dentistry, University of Bergen, Bergen, Norway
- Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway
| | - Frode Selheim
- Proteomics Unit, Department of Biomedicine, Faculty of Medicine and Dentistry, University of Bergen, Bergen, Norway
| | - Frode Berven
- Proteomics Unit, Department of Biomedicine, Faculty of Medicine and Dentistry, University of Bergen, Bergen, Norway
| | - Øystein Bruserud
- Department of Clinical Science, Faculty of Medicine and Dentistry, University of Bergen, Bergen, Norway
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32
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Qi X, Chang C, Xu X, Zhang Y, Bai Y, Liu H. Magnetization of 3-dimentional homochiral metal-organic frameworks for efficient and highly selective capture of phosphopeptides. J Chromatogr A 2016; 1468:49-54. [DOI: 10.1016/j.chroma.2016.09.046] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 09/20/2016] [Accepted: 09/21/2016] [Indexed: 11/16/2022]
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33
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Hernandez-Valladares M, Aasebø E, Selheim F, Berven FS, Bruserud Ø. Selecting Sample Preparation Workflows for Mass Spectrometry-Based Proteomic and Phosphoproteomic Analysis of Patient Samples with Acute Myeloid Leukemia. Proteomes 2016; 4:proteomes4030024. [PMID: 28248234 PMCID: PMC5217354 DOI: 10.3390/proteomes4030024] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 08/09/2016] [Accepted: 08/12/2016] [Indexed: 12/31/2022] Open
Abstract
Global mass spectrometry (MS)-based proteomic and phosphoproteomic studies of acute myeloid leukemia (AML) biomarkers represent a powerful strategy to identify and confirm proteins and their phosphorylated modifications that could be applied in diagnosis and prognosis, as a support for individual treatment regimens and selection of patients for bone marrow transplant. MS-based studies require optimal and reproducible workflows that allow a satisfactory coverage of the proteome and its modifications. Preparation of samples for global MS analysis is a crucial step and it usually requires method testing, tuning and optimization. Different proteomic workflows that have been used to prepare AML patient samples for global MS analysis usually include a standard protein in-solution digestion procedure with a urea-based lysis buffer. The enrichment of phosphopeptides from AML patient samples has previously been carried out either with immobilized metal affinity chromatography (IMAC) or metal oxide affinity chromatography (MOAC). We have recently tested several methods of sample preparation for MS analysis of the AML proteome and phosphoproteome and introduced filter-aided sample preparation (FASP) as a superior methodology for the sensitive and reproducible generation of peptides from patient samples. FASP-prepared peptides can be further fractionated or IMAC-enriched for proteome or phosphoproteome analyses. Herein, we will review both in-solution and FASP-based sample preparation workflows and encourage the use of the latter for the highest protein and phosphorylation coverage and reproducibility.
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Affiliation(s)
- Maria Hernandez-Valladares
- Department of Biomedicine, Faculty of Medicine and Dentistry, University of Bergen, Jonas Lies vei 91, N-5009 Bergen, Norway.
| | - Elise Aasebø
- Department of Biomedicine, Faculty of Medicine and Dentistry, University of Bergen, Jonas Lies vei 91, N-5009 Bergen, Norway.
| | - Frode Selheim
- Department of Biomedicine, Faculty of Medicine and Dentistry, University of Bergen, Jonas Lies vei 91, N-5009 Bergen, Norway.
| | - Frode S Berven
- Department of Biomedicine, Faculty of Medicine and Dentistry, University of Bergen, Jonas Lies vei 91, N-5009 Bergen, Norway.
| | - Øystein Bruserud
- Department of Clinical Science, Faculty of Medicine and Dentistry, University of Bergen, Jonas Lies vei 91, N-5009 Bergen, Norway.
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Aasebø E, Mjaavatten O, Vaudel M, Farag Y, Selheim F, Berven F, Bruserud Ø, Hernandez-Valladares M. Freezing effects on the acute myeloid leukemia cell proteome and phosphoproteome revealed using optimal quantitative workflows. J Proteomics 2016; 145:214-225. [DOI: 10.1016/j.jprot.2016.03.049] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2016] [Revised: 03/23/2016] [Accepted: 03/29/2016] [Indexed: 12/12/2022]
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