1
|
Chin HS, Ravi Varadharajulu N, Lin ZH, Hsu CC, Yu SSF. Phosphoproteomic analysis reveals distinctive responses in Mangrovibacter phragmatis under high-salinity condition. Biochem Biophys Res Commun 2024; 736:150514. [PMID: 39128267 DOI: 10.1016/j.bbrc.2024.150514] [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: 08/01/2024] [Revised: 08/02/2024] [Accepted: 08/06/2024] [Indexed: 08/13/2024]
Abstract
We conducted a thorough genome-wide investigation of protein phosphorylation in the halotolerant bacterium Mangrovibacter phragmitis (MPH) ASIOC01, using the Fe-IMAC enrichment method combined with tandem mass spectrometry under low- and high-salinity conditions. The phosphoproteome comprises 86 unique phosphorylated proteins, crucially involving pathways such as glycolysis/gluconeogenesis, the citrate cycle, chaperones, ribosomal proteins, and cell division. This study represents the first and most extensive investigation to-date comparing the bacterial phosphoproteome under different osmotic conditions using a gel-free approach. We identified 45 unique phosphoproteins in MPH cultured in media containing 1 % NaCl, and 33 exclusive phosphoproteins in MPH cultured in media containing 5 % NaCl. Eight phosphoproteins were detected in both growth conditions. Analysis of high-confidence phosphosites reveals that phosphorylation predominantly occurs on serine residues (52.3 %), followed by threonine (35.1 %) and tyrosine (12.6 %) residues. Interestingly, 34 % of the phosphopeptides display multiple phosphosites. Currently, prokaryotic phosphorylation site prediction platforms like MPSite and NetPhosBac 1.0 demonstrate an average prediction accuracy of only 21 % when applied to our dataset. Fourteen phosphoproteins did not yield matches when compared against dbPSP 2.0 (database of Phosphorylation Sites in Prokaryotes), indicating that these proteins may be novel phosphoproteins. These unique proteins undergoing phosphorylation under high salinity growth conditions potentially enhance their adaptive capabilities to environmental challenges.
Collapse
Affiliation(s)
- Hong Soon Chin
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan; Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan; Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Narendrakumar Ravi Varadharajulu
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan; Molecular Science and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan; Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan
| | - Zhi-Han Lin
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan; Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Chuan-Chih Hsu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Steve S-F Yu
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan; Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan; Molecular Science and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan.
| |
Collapse
|
2
|
Oliinyk D, Will A, Schneidmadel FR, Böhme M, Rinke J, Hochhaus A, Ernst T, Hahn N, Geis C, Lubeck M, Raether O, Humphrey SJ, Meier F. µPhos: a scalable and sensitive platform for high-dimensional phosphoproteomics. Mol Syst Biol 2024; 20:972-995. [PMID: 38907068 PMCID: PMC11297287 DOI: 10.1038/s44320-024-00050-9] [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: 08/25/2023] [Revised: 06/06/2024] [Accepted: 06/11/2024] [Indexed: 06/23/2024] Open
Abstract
Mass spectrometry has revolutionized cell signaling research by vastly simplifying the analysis of many thousands of phosphorylation sites in the human proteome. Defining the cellular response to perturbations is crucial for further illuminating the functionality of the phosphoproteome. Here we describe µPhos ('microPhos'), an accessible phosphoproteomics platform that permits phosphopeptide enrichment from 96-well cell culture and small tissue amounts in <8 h total processing time. By greatly minimizing transfer steps and liquid volumes, we demonstrate increased sensitivity, >90% selectivity, and excellent quantitative reproducibility. Employing highly sensitive trapped ion mobility mass spectrometry, we quantify ~17,000 Class I phosphosites in a human cancer cell line using 20 µg starting material, and confidently localize ~6200 phosphosites from 1 µg. This depth covers key signaling pathways, rendering sample-limited applications and perturbation experiments with hundreds of samples viable. We employ µPhos to study drug- and time-dependent response signatures in a leukemia cell line, and by quantifying 30,000 Class I phosphosites in the mouse brain we reveal distinct spatial kinase activities in subregions of the hippocampal formation.
Collapse
Affiliation(s)
- Denys Oliinyk
- Functional Proteomics, Jena University Hospital, 07747, Jena, Germany
- Comprehensive Cancer Center Central Germany, 07747, Jena, Germany
| | - Andreas Will
- Functional Proteomics, Jena University Hospital, 07747, Jena, Germany
- Comprehensive Cancer Center Central Germany, 07747, Jena, Germany
| | - Felix R Schneidmadel
- Functional Proteomics, Jena University Hospital, 07747, Jena, Germany
- Comprehensive Cancer Center Central Germany, 07747, Jena, Germany
| | - Maximilian Böhme
- Comprehensive Cancer Center Central Germany, 07747, Jena, Germany
- Klinik für Innere Medizin II, Jena University Hospital, 07747, Jena, Germany
| | - Jenny Rinke
- Comprehensive Cancer Center Central Germany, 07747, Jena, Germany
- Klinik für Innere Medizin II, Jena University Hospital, 07747, Jena, Germany
| | - Andreas Hochhaus
- Comprehensive Cancer Center Central Germany, 07747, Jena, Germany
- Klinik für Innere Medizin II, Jena University Hospital, 07747, Jena, Germany
| | - Thomas Ernst
- Comprehensive Cancer Center Central Germany, 07747, Jena, Germany
- Klinik für Innere Medizin II, Jena University Hospital, 07747, Jena, Germany
| | - Nina Hahn
- Section of Translational Neuroimmunology, Department of Neurology, Jena University Hospital, 07747, Jena, Germany
- Center for Sepsis Control and Care, Jena University Hospital, 07747, Jena, Germany
| | - Christian Geis
- Section of Translational Neuroimmunology, Department of Neurology, Jena University Hospital, 07747, Jena, Germany
- Center for Sepsis Control and Care, Jena University Hospital, 07747, Jena, Germany
| | - Markus Lubeck
- Bruker Daltonics GmbH & Co. KG, 28359, Bremen, Germany
| | | | - Sean J Humphrey
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, 3052, Victoria, Australia.
| | - Florian Meier
- Functional Proteomics, Jena University Hospital, 07747, Jena, Germany.
- Comprehensive Cancer Center Central Germany, 07747, Jena, Germany.
| |
Collapse
|
3
|
Donndelinger DV, Yan T, Scoggins TR, Specker JT, Prentice BM. Sequencing of Phosphopeptides Using a Sequential Charge Inversion Ion/Ion Reaction and Electron Capture Dissociation Workflow. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:1556-1566. [PMID: 38806410 DOI: 10.1021/jasms.4c00147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2024]
Abstract
Protein phosphorylation, a common post-translational modification (PTM), is fundamental in a plethora of biological processes, most importantly in modulating cell signaling pathways. Matrix-assisted laser desorption/ionization (MALDI) coupled to tandem mass spectrometry (MS/MS) is an attractive method for phosphopeptide characterization due to its high speed, low limit of detection, and surface sampling capabilities. However, MALDI analysis of phosphopeptides is constrained by relatively low abundances in biological samples and poor relative ionization efficiencies in positive ion mode. Additionally, MALDI tends to produce singly charged ions, generally limiting the accessible MS/MS techniques that can be used for peptide sequencing. For example, collision induced dissociation (CID) is readily amendable to the analysis of singly charged ions, but results in facile loss of phosphoric acid, precluding the localization of the PTM. Electron-based dissociation methods (e.g., electron capture dissociation, ECD) are well suited for PTM localization, but require multiply charged peptide cations to avoid neutralization during ECD. Conversely, phosphopeptides are readily ionized using MALDI in negative ion mode. If the precursor ions are first formed in negative ion mode, a gas-phase charge inversion ion/ion reaction could then be used to transform the phosphopeptide anions produced via MALDI into multiply charged cations that are well-suited for ECD. Herein we demonstrate a multistep workflow combining a charge inversion ion/ion reaction that first transforms MALDI-generated phosphopeptide monoanions into multiply charged cations, and then subjects these multiply charged phosphopeptide cations to ECD for sequence determination and phosphate bond localization.
Collapse
Affiliation(s)
- David V Donndelinger
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Tingting Yan
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Troy R Scoggins
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Jonathan T Specker
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Boone M Prentice
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| |
Collapse
|
4
|
Hansen SSK, Krautz R, Rago D, Havelund J, Stigliani A, Færgeman NJ, Prézelin A, Rivière J, Couturier-Tarrade A, Akimov V, Blagoev B, Elfving B, Neess D, Vogel U, Khodosevich K, Hougaard KS, Sandelin A. Pulmonary maternal immune activation does not cross the placenta but leads to fetal metabolic adaptation. Nat Commun 2024; 15:4711. [PMID: 38830841 PMCID: PMC11148039 DOI: 10.1038/s41467-024-48492-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 04/29/2024] [Indexed: 06/05/2024] Open
Abstract
The fetal development of organs and functions is vulnerable to perturbation by maternal inflammation which may increase susceptibility to disorders after birth. Because it is not well understood how the placenta and fetus respond to acute lung- inflammation, we characterize the response to maternal pulmonary lipopolysaccharide exposure across 24 h in maternal and fetal organs using multi-omics, imaging and integrative analyses. Unlike maternal organs, which mount strong inflammatory immune responses, the placenta upregulates immuno-modulatory genes, in particular the IL-6 signaling suppressor Socs3. Similarly, we observe no immune response in the fetal liver, which instead displays metabolic changes, including increases in lipids containing docosahexaenoic acid, crucial for fetal brain development. The maternal liver and plasma display similar metabolic alterations, potentially increasing bioavailability of docosahexaenoic acid for the mother and fetus. Thus, our integrated temporal analysis shows that systemic inflammation in the mother leads to a metabolic perturbation in the fetus.
Collapse
Affiliation(s)
- Signe Schmidt Kjølner Hansen
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark.
- National Research Centre for the Working Environment, Copenhagen, Denmark.
| | - Robert Krautz
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Daria Rago
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
| | - Jesper Havelund
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Arnaud Stigliani
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
| | - Nils J Færgeman
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Audrey Prézelin
- Université Paris-Saclay, UVSQ, INRAE, BREED, 78350, Jouy-en-Josas, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France
| | - Julie Rivière
- Paris-Saclay University, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
- Paris-Saclay University, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Anne Couturier-Tarrade
- Université Paris-Saclay, UVSQ, INRAE, BREED, 78350, Jouy-en-Josas, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France
| | - Vyacheslav Akimov
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Blagoy Blagoev
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Betina Elfving
- Translational Neuropsychiatry Unit, Aarhus University, Aarhus, Denmark
| | - Ditte Neess
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Ulla Vogel
- National Research Centre for the Working Environment, Copenhagen, Denmark
| | - Konstantin Khodosevich
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
| | - Karin Sørig Hougaard
- National Research Centre for the Working Environment, Copenhagen, Denmark.
- Department of Public Health, University of Copenhagen, Copenhagen, Denmark.
| | - Albin Sandelin
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark.
| |
Collapse
|
5
|
Wu C, Zhang S, Hou C, Byers S, Ma J. In-Depth Endogenous Phosphopeptidomics of Serum with Zirconium(IV)-Grafted Mesoporous Silica Enrichment. Anal Chem 2024; 96:8254-8262. [PMID: 38728223 PMCID: PMC11140682 DOI: 10.1021/acs.analchem.3c02150] [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: 05/17/2023] [Revised: 03/21/2024] [Accepted: 04/22/2024] [Indexed: 05/12/2024]
Abstract
Detection of endogenous peptides, especially those with modifications (such as phosphorylation) in biofluids, can serve as an indicator of intracellular pathophysiology. Although great progress has been made in phosphoproteomics in recent years, endogenous phosphopeptidomics has largely lagged behind. One main hurdle in endogenous phosphopeptidomics analysis is the coexistence of proteins and highly abundant nonmodified peptides in complex matrices. In this study, we developed an approach using zirconium(IV)-grafted mesoporous beads to enrich phosphopeptides, followed by analysis with a high resolution nanoRPLC-MS/MS system. The bifunctional material was first tested with digests of standard phosphoproteins and HeLa cell lysates, with excellent enrichment performance achieved. Given the size exclusion nature, the beads were directly applied for endogenous phosphopeptidomic analysis of serum samples from pancreatic ductal adenocarcinoma (PDAC) patients and controls. In total, 329 endogenous phosphopeptides (containing 113 high confidence sites) were identified across samples, by far the largest endogenous phosphopeptide data set cataloged to date. In addition, the method was readily applied for phosphoproteomics of the same set of samples, with 172 phosphopeptides identified and significant changes in dozens of phosphopeptides observed. Given the simplicity and robustness of the proposed method, we envision that it can be readily used for comprehensive phosphorylation studies of serum and other biofluid samples.
Collapse
Affiliation(s)
- Ci Wu
- Department
of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington D.C. 20007, United States
- School
of Chemistry and Chemical Engineering, Liaoning
Normal University, Dalian 116029, China
| | - Shen Zhang
- Clinical
Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-XIANGYA, Changsha 410000, China
| | - Chunyan Hou
- Department
of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington D.C. 20007, United States
| | - Stephen Byers
- Department
of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington D.C. 20007, United States
| | - Junfeng Ma
- Department
of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington D.C. 20007, United States
| |
Collapse
|
6
|
Bortel P, Piga I, Koenig C, Gerner C, Martinez-Val A, Olsen JV. Systematic Optimization of Automated Phosphopeptide Enrichment for High-Sensitivity Phosphoproteomics. Mol Cell Proteomics 2024; 23:100754. [PMID: 38548019 PMCID: PMC11087715 DOI: 10.1016/j.mcpro.2024.100754] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 03/08/2024] [Accepted: 03/22/2024] [Indexed: 05/05/2024] Open
Abstract
Improving coverage, robustness, and sensitivity is crucial for routine phosphoproteomics analysis by single-shot liquid chromatography-tandem mass spectrometry (LC-MS/MS) from minimal peptide inputs. Here, we systematically optimized key experimental parameters for automated on-bead phosphoproteomics sample preparation with a focus on low-input samples. Assessing the number of identified phosphopeptides, enrichment efficiency, site localization scores, and relative enrichment of multiply-phosphorylated peptides pinpointed critical variables influencing the resulting phosphoproteome. Optimizing glycolic acid concentration in the loading buffer, percentage of ammonium hydroxide in the elution buffer, peptide-to-beads ratio, binding time, sample, and loading buffer volumes allowed us to confidently identify >16,000 phosphopeptides in half-an-hour LC-MS/MS on an Orbitrap Exploris 480 using 30 μg of peptides as starting material. Furthermore, we evaluated how sequential enrichment can boost phosphoproteome coverage and showed that pooling fractions into a single LC-MS/MS analysis increased the depth. We also present an alternative phosphopeptide enrichment strategy based on stepwise addition of beads thereby boosting phosphoproteome coverage by 20%. Finally, we applied our optimized strategy to evaluate phosphoproteome depth with the Orbitrap Astral MS using a cell dilution series and were able to identify >32,000 phosphopeptides from 0.5 million HeLa cells in half-an-hour LC-MS/MS using narrow-window data-independent acquisition (nDIA).
Collapse
Affiliation(s)
- Patricia Bortel
- Faculty of Chemistry, Department of Analytical Chemistry, University of Vienna, Vienna, Austria; Vienna Doctoral School in Chemistry (DoSChem), University of Vienna, Vienna, Austria
| | - Ilaria Piga
- Proteomics Program, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Claire Koenig
- Proteomics Program, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Christopher Gerner
- Faculty of Chemistry, Department of Analytical Chemistry, University of Vienna, Vienna, Austria; Joint Metabolome Facility, University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Ana Martinez-Val
- Proteomics Program, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark.
| | - Jesper V Olsen
- Proteomics Program, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark.
| |
Collapse
|
7
|
Abel NB, Nørgaard MMM, Hansen SB, Gysel K, Díez IA, Jensen ON, Stougaard J, Andersen KR. Phosphorylation of the alpha-I motif in SYMRK drives root nodule organogenesis. Proc Natl Acad Sci U S A 2024; 121:e2311522121. [PMID: 38363863 PMCID: PMC10895371 DOI: 10.1073/pnas.2311522121] [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: 07/07/2023] [Accepted: 12/15/2023] [Indexed: 02/18/2024] Open
Abstract
Symbiosis receptor-like kinase SYMRK is required for root nodule symbiosis between legume plants and nitrogen-fixing bacteria. To understand symbiotic signaling from SYMRK, we determined the crystal structure to 1.95 Å and mapped the phosphorylation sites onto the intracellular domain. We identified four serine residues in a conserved "alpha-I" motif, located on the border between the kinase core domain and the flexible C-terminal tail, that, when phosphorylated, drives organogenesis. Substituting the four serines with alanines abolished symbiotic signaling, while substituting them with phosphorylation-mimicking aspartates induced the formation of spontaneous nodules in the absence of bacteria. These findings show that the signaling pathway controlling root nodule organogenesis is mediated by SYMRK phosphorylation, which may help when engineering this trait into non-legume plants.
Collapse
Affiliation(s)
- Nikolaj B. Abel
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C8000, Denmark
| | - Malita M. M. Nørgaard
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C8000, Denmark
| | - Simon B. Hansen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C8000, Denmark
| | - Kira Gysel
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C8000, Denmark
| | - Ignacio Arribas Díez
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M5230, Denmark
| | - Ole N. Jensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M5230, Denmark
| | - Jens Stougaard
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C8000, Denmark
| | - Kasper R. Andersen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C8000, Denmark
| |
Collapse
|
8
|
Lim Kam Sian TCC, Sun C, Cain JE, Steele JR, Hanchapola I, Stoychev S, Schittenhelm RB, Faridi P. A Semiautomated Proteomics and Phosphoproteomics Protocol for the Identification of Novel Therapeutic Targets and Predictive Biomarkers in In Vivo Xenograft Models of Pediatric Cancers. Methods Mol Biol 2024; 2806:229-242. [PMID: 38676807 DOI: 10.1007/978-1-0716-3858-3_17] [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: 04/29/2024]
Abstract
Genomic profiling has identified therapeutic targets for precision treatment of certain cancers, but many patients lack actionable mutations. Additional omics approaches, like proteomics and phosphoproteomics, are essential for comprehensive mapping of cancer-associated molecular phenotypes. In vivo models, such as cell line and patient-derived xenografts (PDX), offer valuable insights into cancer biology and treatment strategies.This chapter presents a semiautomated high-throughput workflow for integrated proteomics and phosphoproteomics analysis on the Kingfish platform coupled with MagReSyn® Zr-IMAC HP. It enhances protein extraction from in vivo xenograft samples and provides better insights into cancers with poor prognosis. The approach successfully identified over 11,000 unique phosphosites and ~6000 proteins in SJSA-1 pediatric osteosarcoma xenografts, demonstrating its efficacy. This workflow is a valuable tool for studying tumor biology and developing precision oncology strategies.
Collapse
Affiliation(s)
- Terry C C Lim Kam Sian
- Monash Proteomics and Metabolomics Platform, Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- Department of Medicine, Sub-Faculty of Clinical and Molecular Medicine, Faculty of Medicine, Nursing & Health Sciences, Monash University, Clayton, VIC, Australia
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Molecular and Translational Medicine, School of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC, Australia
| | - Christie Sun
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Molecular and Translational Medicine, School of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC, Australia
| | - Jason E Cain
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Molecular and Translational Medicine, School of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC, Australia
| | - Joel R Steele
- Monash Proteomics and Metabolomics Platform, Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Iresha Hanchapola
- Monash Proteomics and Metabolomics Platform, Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | | | - Ralf B Schittenhelm
- Monash Proteomics and Metabolomics Platform, Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.
| | - Pouya Faridi
- Monash Proteomics and Metabolomics Platform, Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.
- Department of Medicine, Sub-Faculty of Clinical and Molecular Medicine, Faculty of Medicine, Nursing & Health Sciences, Monash University, Clayton, VIC, Australia.
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, VIC, Australia.
- Department of Molecular and Translational Medicine, School of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC, Australia.
| |
Collapse
|
9
|
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.
Collapse
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.
| |
Collapse
|
10
|
Luo W, van Beek TA, Chen B, Zuilhof H, Salentijn GI. Bifunctional Ti 4+-modified paper for selective extraction or removal of phospholipids and paper spray mass spectrometry for bioanalysis in urine and plasma. Anal Chim Acta 2023; 1278:341673. [PMID: 37709425 DOI: 10.1016/j.aca.2023.341673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 07/28/2023] [Accepted: 07/29/2023] [Indexed: 09/16/2023]
Abstract
BACKGROUND Phospholipids (PLs) are major constituents of cell membranes, play important roles in cell proliferation and death, as well as in signal transduction, and therefore are relevant biomarkers for different pathologies. On the other hand, when the analysis of small compounds, such as therapeutics in blood is desired, then phospholipids are part of the matrix and cause serious interference during analysis. Currently, both the analysis and removal of PLs from biological samples are limited by extensive sample preparation and instrumental separation. RESULTS A fast and simple quantitative Ti4+-modified paper spray tandem mass spectrometric (TiPS-MS/MS) method was established in urine, where the enrichment of phospholipids was achieved, as well as reduction of matrix effects (primarily caused by high salt content) that ultimately led to improved sensitivity and selectivity. The method could achieve a physiologically relevant limit of detection (0.01-0.03 μg mL-1). Also, the usefulness of the Ti4+-modified paper was investigated in the opposite mode, namely for the selective removal of phospholipids from matrices such as plasma. Clonidine is used as model compound, as the detection of this compound is known to suffer from ion suppression by phospholipids. Compared with blank paper spray tandem mass spectrometry, the limit of detection could be improved from 0.3 μg mL-1 to 0.03 μg mL-1 by employing a Ti4+-modified paper on top of the spray tip to capture phospholipids from the sample. SIGNIFICANCE AND NOVELTY A novel Ti4+-modified paper was developed to allow for rapid solid-phase extraction of phospholipids from urine or selective removal from plasma, followed by direct paper spray mass spectrometric detection as a fast and convenient sample preparation and analysis combination. The paper properties are based on the Ti4+ metal ion, which can selectively bind phosphate-containing compounds under acidic conditions, and its applicability was demonstrated in relevant biological matrices.
Collapse
Affiliation(s)
- Wei Luo
- Key Laboratory of Phytochemical R&D of Hunan Province and Key Laboratory of Chemical Biology & Traditional Chinese Medicine Research of Ministry of Education, Hunan Normal University, Changsha, 410081, China; Laboratory of Organic Chemistry, Wageningen University, 6708, WE Wageningen, the Netherlands
| | - Teris A van Beek
- Laboratory of Organic Chemistry, Wageningen University, 6708, WE Wageningen, the Netherlands
| | - Bo Chen
- Key Laboratory of Phytochemical R&D of Hunan Province and Key Laboratory of Chemical Biology & Traditional Chinese Medicine Research of Ministry of Education, Hunan Normal University, Changsha, 410081, China.
| | - Han Zuilhof
- Key Laboratory of Phytochemical R&D of Hunan Province and Key Laboratory of Chemical Biology & Traditional Chinese Medicine Research of Ministry of Education, Hunan Normal University, Changsha, 410081, China; Laboratory of Organic Chemistry, Wageningen University, 6708, WE Wageningen, the Netherlands.
| | - Gert Ij Salentijn
- Laboratory of Organic Chemistry, Wageningen University, 6708, WE Wageningen, the Netherlands; Wageningen Food Safety Research (WFSR), Wageningen University & Research, 6700, AE Wageningen, the Netherlands.
| |
Collapse
|
11
|
Martínez-Val A, Fort K, Koenig C, Van der Hoeven L, Franciosa G, Moehring T, Ishihama Y, Chen YJ, Makarov A, Xuan Y, Olsen JV. Hybrid-DIA: intelligent data acquisition integrates targeted and discovery proteomics to analyze phospho-signaling in single spheroids. Nat Commun 2023; 14:3599. [PMID: 37328457 PMCID: PMC10276052 DOI: 10.1038/s41467-023-39347-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 06/06/2023] [Indexed: 06/18/2023] Open
Abstract
Achieving sufficient coverage of regulatory phosphorylation sites by mass spectrometry (MS)-based phosphoproteomics for signaling pathway reconstitution is challenging, especially when analyzing tiny sample amounts. To address this, we present a hybrid data-independent acquisition (DIA) strategy (hybrid-DIA) that combines targeted and discovery proteomics through an Application Programming Interface (API) to dynamically intercalate DIA scans with accurate triggering of multiplexed tandem mass spectrometry (MSx) scans of predefined (phospho)peptide targets. By spiking-in heavy stable isotope labeled phosphopeptide standards covering seven major signaling pathways, we benchmark hybrid-DIA against state-of-the-art targeted MS methods (i.e., SureQuant) using EGF-stimulated HeLa cells and find the quantitative accuracy and sensitivity to be comparable while hybrid-DIA also profiles the global phosphoproteome. To demonstrate the robustness, sensitivity, and biomedical potential of hybrid-DIA, we profile chemotherapeutic agents in single colon carcinoma multicellular spheroids and evaluate the phospho-signaling difference of cancer cells in 2D vs 3D culture.
Collapse
Affiliation(s)
- Ana Martínez-Val
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Kyle Fort
- Thermo Fisher Scientific, Bremen, Germany
| | - Claire Koenig
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Leander Van der Hoeven
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Giulia Franciosa
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | | | | | | | | | - Yue Xuan
- Thermo Fisher Scientific, Bremen, Germany.
| | - Jesper V Olsen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark.
| |
Collapse
|
12
|
Wang K, Yu A, Gao Y, Chen M, Yuan H, Zhang S, Ouyang G. A nitrogen-doped graphene tube composite based on immobilized metal affinity chromatography for the capture of phosphopeptides. Talanta 2023; 261:124617. [PMID: 37187026 DOI: 10.1016/j.talanta.2023.124617] [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: 03/28/2023] [Revised: 04/24/2023] [Accepted: 04/28/2023] [Indexed: 05/17/2023]
Abstract
A novel immobilized metal affinity chromatography (IMAC) functional composite, mNi@N-GrT@PDA@Ti4+, was fabricated based on ultrathin magnetic nitrogen-doped graphene tube (mNi@N-GrT) after chelated Ti4+ with polydopamine, following as a magnetic solid-phase extraction sorbent for rapidly selective enrichment and mass spectrometry identification of phosphorylated peptides. After optimized, the composite exhibited high specificity in the enrichment of phosphopeptides from the digest mixture of β-casein and bovine serum albumin (BSA). The robust method presented the low detection limits (1 fmol, 200 μL) and excellent selectivity (1:100) in the molar ration mixture of β-casein and BSA digests. Furthermore, the selective enrichment of phosphopeptides in the complex bio-samples, was successfully carried out. The results showed that 28 phosphopeptides were finally detected in mouse brain, and 2087 phosphorylated peptides were identified in the HeLa cells extracts with specific selectivity of 95.6%. The enrichment performance of mNi@N-GrT@PDA@Ti4+ was satisfactory, suggesting that the functional composite provided a potential application in the enrichment of trace phosphorylated peptides from the complex biological matrix.
Collapse
Affiliation(s)
- Kexuan Wang
- College of Chemistry, Key Laboratory of Molecular Sensing and Harmful Substances Detection Technology, Zhengzhou University, Kexue Avenue 100, Zhengzhou, Henan, 450001, PR China
| | - Ajuan Yu
- College of Chemistry, Key Laboratory of Molecular Sensing and Harmful Substances Detection Technology, Zhengzhou University, Kexue Avenue 100, Zhengzhou, Henan, 450001, PR China.
| | - Yu Gao
- High & New Technology Research Center of Henan Academy of Sciences, Zhengzhou, Henan Province, 450002, PR China
| | - Miao Chen
- College of Chemistry, Key Laboratory of Molecular Sensing and Harmful Substances Detection Technology, Zhengzhou University, Kexue Avenue 100, Zhengzhou, Henan, 450001, PR China
| | - Hang Yuan
- Center of Advanced Analysis and Gene Sequencing, Key Laboratory of Molecular Sensing and Harmful Substances Detection Technology, Zhengzhou University, Kexue Avenue 100, Zhengzhou, Henan, 450001, PR China
| | - Shusheng Zhang
- Center of Advanced Analysis and Gene Sequencing, Key Laboratory of Molecular Sensing and Harmful Substances Detection Technology, Zhengzhou University, Kexue Avenue 100, Zhengzhou, Henan, 450001, PR China.
| | - Gangfeng Ouyang
- Center of Advanced Analysis and Gene Sequencing, Key Laboratory of Molecular Sensing and Harmful Substances Detection Technology, Zhengzhou University, Kexue Avenue 100, Zhengzhou, Henan, 450001, PR China
| |
Collapse
|
13
|
Zhang X, Gao J, Wei T, Wu D, Shen J, Wei Y, Wang C. Polymer brush grafted immobilized metal ion affinity adsorbent based on polydopamine/polyethyleneimine-coated magnetic graphene oxide for selective enrichment of cytokinins in plants. Mikrochim Acta 2023; 190:191. [PMID: 37099040 DOI: 10.1007/s00604-023-05776-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 03/31/2023] [Indexed: 04/27/2023]
Abstract
An immobilized metal affinity (IMAC) adsorbent was prepared for selective enrichment of adenine type CKs, via grafting polymer chain pendant with iminodiacetic acid (IDA) from polydopamine (PDA)/polyethyleneimine (PEI)-coated magnetic graphene oxide (magGO) via surface-initiated-atom transfer radical polymerization (SI-ATRP). The prepared IMAC sorbent exhibited remarkable adsorption performances and good selectivity for adenine-type CKs and was utilized as a sorbent of magnetic solid-phase extraction (MSPE) for effective enrichment of four adenine-type CKs in bean sprouts. Under the optimized extraction conditions, an analytical method for four adenine type CKs in bean sprouts was established by combining the MSPE combined with ultra-high-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS). The recoveries of the analytes were between 80.4 ± 1.9% and 114.6 ± 1.5% (n = 3). The limits of detection (LODs) range from 0.63 to 2.30 pg⋅mL-1. The relative standard deviations of intra-day and inter-day were less than 12.6%. The established method was successfully applied to the selective extraction and sensitive detection of trace adenine-type CKs in plant samples.
Collapse
Affiliation(s)
- Xiaoxia Zhang
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, 1 Xue Fu Avenue, Chang'an District, Xi'an, 710127, China
| | - Jingnan Gao
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, 1 Xue Fu Avenue, Chang'an District, Xi'an, 710127, China
| | - Tong Wei
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, 1 Xue Fu Avenue, Chang'an District, Xi'an, 710127, China
| | - Dan Wu
- Sunresin New Materials Co., Ltd., Xi'an, People's Republic of China
| | - Jiwei Shen
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, 1 Xue Fu Avenue, Chang'an District, Xi'an, 710127, China
| | - Yinmao Wei
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, 1 Xue Fu Avenue, Chang'an District, Xi'an, 710127, China
| | - Chaozhan Wang
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, 1 Xue Fu Avenue, Chang'an District, Xi'an, 710127, China.
| |
Collapse
|
14
|
Xie Z, Feng Q, Zhang S, Yan Y, Deng C, Ding CF. Advances in proteomics sample preparation and enrichment for phosphorylation and glycosylation analysis. Proteomics 2022; 22:e2200070. [PMID: 36100958 DOI: 10.1002/pmic.202200070] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 08/06/2022] [Accepted: 08/15/2022] [Indexed: 11/08/2022]
Abstract
As the common and significant chemical modifications, post-translational modifications (PTMs) play a key role in the functional proteome. Affected by the signal interference, low concentration, and insufficient ionization efficiency of impurities, the direct detection of PTMs by mass spectrometry (MS) still faces many challenges. Therefore, sample preparation and enrichment are an indispensable link before MS analysis of PTMs in proteomics. The rapid development of functionalized materials with diverse morphologies and compositions provides an avenue for sample preparation and enrichment for PTMs analysis. In this review, we summarize recent advances in the application of novel functionalized materials in sample preparation for phosphoproteomes and glycoproteomes analysis. In addition, this review specifically discusses the design and preparation of functionalized materials based on different enrichment mechanisms, and proposes research directions and potential challenges for proteomic PTMs research.
Collapse
Affiliation(s)
- Zehu Xie
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang, China
| | - Quanshou Feng
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang, China
| | - Shun Zhang
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang, China
| | - Yinghua Yan
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang, China.,Department of Experimental Medical Science, HwaMei Hospital, University of Chinese Academy of Sciences, Ningbo, Zhejiang, China
| | - Chunhui Deng
- Department of Chemistry, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Chuan-Fan Ding
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang, China.,Department of Experimental Medical Science, HwaMei Hospital, University of Chinese Academy of Sciences, Ningbo, Zhejiang, China
| |
Collapse
|
15
|
Materials, workflows and applications of IMAC for phosphoproteome profiling in the recent decade: A review. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
16
|
Alonso-Fernández S, Arribas-Díez I, Fernández-García G, González-Quiñónez N, Jensen ON, Manteca A. Quantitative phosphoproteome analysis of Streptomyces coelicolor by immobilized zirconium (IV) affinity chromatography and mass spectrometry reveals novel regulated protein phosphorylation sites and sequence motifs. J Proteomics 2022; 269:104719. [PMID: 36089190 DOI: 10.1016/j.jprot.2022.104719] [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: 06/07/2022] [Revised: 08/25/2022] [Accepted: 09/03/2022] [Indexed: 11/12/2022]
Abstract
Streptomycetes are multicellular gram-positive bacteria that produce many bioactive compounds, including antibiotics, antitumorals and immunosuppressors. The Streptomyces phosphoproteome remains largely uncharted even though protein phosphorylation at Ser/Thr/Tyr is known to modulate morphological differentiation and specialized metabolic processes. We here expand the S. coelicolor phosphoproteome by optimised immobilized zirconium (IV) affinity chromatography and mass spectrometry to identify phosphoproteins at the vegetative and sporulating stages. We mapped 361 phosphorylation sites (41% pSer, 56.2% pThr, 2.8% pTyr) and discovered four novel Thr phosphorylation motifs ("Kxxxx(pT)xxxxK", "DxE(pT)", "D(pT)" and "Exxxxx(pT)") in 351 phosphopeptides derived from 187 phosphoproteins. We identified 154 novel phosphoproteins, thereby almost doubling the number of experimentally verified Streptomyces phosphoproteins. Novel phosphoproteins included cell division proteins (FtsK, CrgA) and specialized metabolism regulators (ArgR, AfsR, CutR and HrcA) that were differentially phosphorylated in the vegetative and in the antibiotic producing sporulating stages. Phosphoproteins involved in primary metabolism included 27 novel ribosomal proteins that were phosphorylated during the vegetative stage. Phosphorylation of these proteins likely participate in the intricate and incompletely understood regulation of Streptomyces development and secondary metabolism. We conclude that Zr(IV)-IMAC is an efficient and sensitive method to study protein phosphorylation and regulation in bacteria and enhance our understanding of bacterial signalling. SIGNIFICANCE: Two thirds of the secondary metabolites used in clinic, especially antibiotics, were discovered in Streptomyces strains. Antibiotic resistance became one of the major challenges in clinic, and new antibiotics are urgently required in clinic. Next-generation sequencing analyses revealed that streptomycetes harbour many cryptic secondary metabolite pathways, i.e. pathways not expressed in the laboratory. Secondary metabolism is tightly connected with hypha differentiation and sporulation, and understanding Streptomyces differentiation is one of the main challenges in industrial microbiology, in order to activate the expression of cryptic pathways in the laboratory. Protein phosphorylation at Ser/Thr/Tyr modulates development and secondary metabolism, but the Streptomyces phosphoproteome is still largely uncharted. Previous S. coelicolor phosphoproteomic studies used TiO2 affinity enrichment and LC-MS/MS identifying a total of 184 Streptomyces phosphoproteins. Here, we used by first time zirconium (IV) affinity chromatography and mass spectrometry, identifying 186 S. coelicolor phosphoproteins. Most of these phosphoproteins (154) were not identified in previous phosphoproteomic studies using TiO2 affinity enrichment. Thereby we almost doubling the number of experimentally verified Streptomyces phosphoproteins. Zr(IV)-IMAC affinity chromatography also worked in E. coli, allowing the identification of phosphoproteins that were not identified by TiO2 affinity chromatography. We conclude that Zr(IV)-IMAC is an efficient and sensitive method for studies of protein phosphorylation and regulation in bacteria to enhance our understanding of bacterial signalling networks. Moreover, the new Streptomyces phosphoproteins identified will contribute to design further works to understand and modulate Streptomyces secondary metabolism activation.
Collapse
Affiliation(s)
- Sergio Alonso-Fernández
- Área de Microbiología, Departamento de Biología Funcional, IUOPA, ISPA, Facultad de Medicina, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Ignacio Arribas-Díez
- Department of Biochemistry and Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Gemma Fernández-García
- Área de Microbiología, Departamento de Biología Funcional, IUOPA, ISPA, Facultad de Medicina, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Nathaly González-Quiñónez
- Área de Microbiología, Departamento de Biología Funcional, IUOPA, ISPA, Facultad de Medicina, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Ole N Jensen
- Department of Biochemistry and Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark.
| | - Angel Manteca
- Área de Microbiología, Departamento de Biología Funcional, IUOPA, ISPA, Facultad de Medicina, Universidad de Oviedo, 33006 Oviedo, Spain.
| |
Collapse
|
17
|
Ouyang M, Wu J, Yan Y, Ding CF. Efficient Enrichment of Global Phosphopeptides Using Magnetic Tannic Acid – Titanium(IV)/Zirconium(IV) Functionalized Spheres as a Novel Sorbent for Immobilized Metal Ion Affinity Chromatography (IMAC). ANAL LETT 2022. [DOI: 10.1080/00032719.2022.2116644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- Menglin Ouyang
- Department of Anesthesiology, The Affiliated Hospital of Medical School, Ningbo University, Ningbo, China
| | - Jiani Wu
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, School of Materials Science and Chemical Engineering, Institute of Mass Spectrometry, Ningbo University, Ningbo, China
| | - Yinghua Yan
- Department of Anesthesiology, The Affiliated Hospital of Medical School, Ningbo University, Ningbo, China
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, School of Materials Science and Chemical Engineering, Institute of Mass Spectrometry, Ningbo University, Ningbo, China
| | - Chuan-Fan Ding
- Department of Anesthesiology, The Affiliated Hospital of Medical School, Ningbo University, Ningbo, China
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, School of Materials Science and Chemical Engineering, Institute of Mass Spectrometry, Ningbo University, Ningbo, China
| |
Collapse
|
18
|
Zeng X, Lan Y, Xiao J, Hu L, Tan L, Liang M, Wang X, Lu S, Peng T, Long F. Advances in phosphoproteomics and its application to COPD. Expert Rev Proteomics 2022; 19:311-324. [PMID: 36730079 DOI: 10.1080/14789450.2023.2176756] [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: 02/03/2023]
Abstract
INTRODUCTION Chronic obstructive pulmonary disease (COPD) was the third leading cause of global death in 2019, causing a huge economic burden to society. Therefore, it is urgent to identify specific phenotypes of COPD patients through early detection, and to promptly treat exacerbations. The field of phosphoproteomics has been a massive advancement, compelled by the developments in mass spectrometry, enrichment strategies, algorithms, and tools. Modern mass spectrometry-based phosphoproteomics allows understanding of disease pathobiology, biomarker discovery, and predicting new therapeutic modalities. AREAS COVERED In this article, we present an overview of phosphoproteomic research and strategies for enrichment and fractionation of phosphopeptides, identification of phosphorylation sites, chromatographic separation and mass spectrometry detection strategies, and the potential application of phosphorylated proteomic analysis in the diagnosis, treatment, and prognosis of COPD disease. EXPERT OPINION The role of phosphoproteomics in COPD is critical for understanding disease pathobiology, identifying potential biomarkers, and predicting new therapeutic approaches. However, the complexity of COPD requires the more comprehensive understanding that can be achieved through integrated multi-omics studies. Phosphoproteomics, as a part of these multi-omics approaches, can provide valuable insights into the underlying mechanisms of COPD.
Collapse
Affiliation(s)
- Xiaoyin Zeng
- Sino-French Hoffmann Institute, School of Basic Medical Science, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
| | - Yanting Lan
- Sino-French Hoffmann Institute, School of Basic Medical Science, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
| | - Jing Xiao
- Sino-French Hoffmann Institute, School of Basic Medical Science, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
| | - Longbo Hu
- Sino-French Hoffmann Institute, School of Basic Medical Science, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
| | - Long Tan
- Sino-French Hoffmann Institute, School of Basic Medical Science, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
| | - Mengdi Liang
- Sino-French Hoffmann Institute, School of Basic Medical Science, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
| | - Xufei Wang
- Sino-French Hoffmann Institute, School of Basic Medical Science, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
| | - Shaohua Lu
- Sino-French Hoffmann Institute, School of Basic Medical Science, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
| | - Tao Peng
- Sino-French Hoffmann Institute, School of Basic Medical Science, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, China.,Guangdong South China Vaccine Co. Ltd, Guangzhou, China
| | - Fei Long
- Sino-French Hoffmann Institute, School of Basic Medical Science, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
| |
Collapse
|
19
|
Identification, production and bioactivity of casein phosphopeptides – A review. Food Res Int 2022; 157:111360. [DOI: 10.1016/j.foodres.2022.111360] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 04/28/2022] [Accepted: 05/10/2022] [Indexed: 01/23/2023]
|
20
|
Comprehensive Evaluation of Different TiO2-Based Phosphopeptide Enrichment and Fractionation Methods for Phosphoproteomics. Cells 2022; 11:cells11132047. [PMID: 35805136 PMCID: PMC9265536 DOI: 10.3390/cells11132047] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 06/24/2022] [Accepted: 06/24/2022] [Indexed: 02/04/2023] Open
Abstract
Protein phosphorylation is an essential post-translational modification that regulates multiple cellular processes. Due to their low stoichiometry and ionization efficiency, it is critical to efficiently enrich phosphopeptides for phosphoproteomics. Several phosphopeptide enrichment methods have been reported; however, few studies have comprehensively compared different TiO2-based phosphopeptide enrichment methods using complex proteomic samples. Here, we compared four TiO2-based phosphopeptide enrichment methods that used four non-phosphopeptide excluders (glutamic acid, lactic acid, glycolic acid, and DHB). We found that these four TiO2-based phosphopeptide enrichment methods had different enrichment specificities and that phosphopeptides enriched by the four methods had different physicochemical characteristics. More importantly, we discovered that phosphopeptides had a higher deamidation ratio than peptides from cell lysate and that phosphopeptides enriched using the glutamic acid method had a higher deamidation ratio than the other three methods. We then compared two phosphopeptide fractionation methods: ammonia- or TEA-based high pH reversed-phase (HpH-RP). We found that fewer phosphopeptides, especially multi-phosphorylated peptides, were identified using the ammonia-based method than using the TEA-based method. Therefore, the TEA-based HpH-RP fractionation method performed better than the ammonia method. In conclusion, we comprehensively evaluated different TiO2-based phosphopeptide enrichment and fractionation methods, providing a basis for selecting the proper protocols for comprehensive phosphoproteomics.
Collapse
|
21
|
Lv X, Jiao S, Wei Z, Cui C, Wang W, Tan Y, Pang G. Preparation of Core‐Shell Structured Magnetic Superhydrophilic Extractant for Enrichment of Phosphopeptides. ChemistrySelect 2022. [DOI: 10.1002/slct.202200821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Xinyan Lv
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry College of Chemistry Jilin University Changchun 130012 P. R. China
| | - Shihui Jiao
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry College of Chemistry Jilin University Changchun 130012 P. R. China
| | - Zhonglin Wei
- Department of Organic Chemistry College of Chemistry Jilin University Changchun 130012 P. R. China
| | - Canyu Cui
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry College of Chemistry Jilin University Changchun 130012 P. R. China
| | - Wenwen Wang
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry College of Chemistry Jilin University Changchun 130012 P. R. China
| | - Yumei Tan
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry College of Chemistry Jilin University Changchun 130012 P. R. China
| | - Guangsheng Pang
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry College of Chemistry Jilin University Changchun 130012 P. R. China
| |
Collapse
|
22
|
He M, Wang J, Herold S, Xi L, Schulze WX. A Rapid and Universal Workflow for Label-Free-Quantitation-Based Proteomic and Phosphoproteomic Studies in Cereals. Curr Protoc 2022; 2:e425. [PMID: 35674286 DOI: 10.1002/cpz1.425] [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: 06/15/2023]
Abstract
Proteomics and phosphoproteomics are robust tools to analyze dynamics of post-transcriptional processes during growth and development. A variety of experimental methods and workflows have been published, but most of them were developed for model plants and have not been adapted to high-throughput platforms. Here, we describe an experimental workflow for proteome and phosphoproteome studies tailored to cereal crop tissues. The workflow consists of two parallel parts that are suitable for analyzing protein/phosphoprotein from total proteins and the microsomal membrane fraction. We present phosphoproteomic data regarding quantification coverage and analytical reproducibility for example preparations from maize root and shoot, wheat leaf, and a microsomal protein preparation from maize leaf. To enable users to adjust for tissue specific requirements, we provide two different methods of protein clean-up: traditional ethanol precipitation (PC) and a recently developed technology termed single-pot, solid-phase-enhanced sample preparation (SP3). Both the PC and SP3 methods are effective in the removal of unwanted substances in total protein crude extracts. In addition, two different methods of phosphopeptide enrichment are presented: a TiO2 -based method and Fe(III)-NTA cartridges on a robotized platform. Although the overall number of phosphopeptides is stable across protein clean-up and phosphopeptide enrichment methods, there are differences in the preferred phosphopeptides in each enrichment method. The preferred protocol depends on laboratory capabilities and research objective. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Total protein crude extraction Basic Protocol 2: Total protein clean-up with ethanol precipitation Alternate Protocol 1: Total protein clean-up with SP3 method Basic Protocol 3: Microsomal fraction protein extraction Basic Protocol 4: Protein concentration determination by Bradford assay Basic Protocol 5: In-solution digestion with trypsin Basic Protocol 6: Phosphopeptide enrichment with TiO2 Alternate Protocol 2: Phosphopeptide enrichment with Fe(III)-NTA cartridges Basic Protocol 7: Peptide desalting with C18 material Basic Protocol 8: LC-MS/MS analysis of (phospho)peptides and spectrum matching.
Collapse
Affiliation(s)
- Mingjie He
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany
| | - Jiahui Wang
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany
| | - Sandra Herold
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany
| | - Lin Xi
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany
| | - Waltraud X Schulze
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany
| |
Collapse
|
23
|
Abstract
Proteins are the molecular effectors of the information encoded in the genome. Proteomics aims at understanding the molecular functions of proteins in their biological context. In contrast to transcriptomics and genomics, the study of proteomes provides deeper insight into the dynamic regulatory layers encoded at the protein level, such as posttranslational modifications, subcellular localization, cell signaling, and protein-protein interactions. Currently, mass spectrometry (MS)-based proteomics is the technology of choice for studying proteomes at a system-wide scale, contributing to clinical biomarker discovery and fundamental molecular biology. MS technologies are continuously being developed to fulfill the requirements of speed, resolution, and quantitative accuracy, enabling the acquisition of comprehensive proteomes. In this review, we present how MS technology and acquisition methods have evolved to meet the requirements of cutting-edge proteomics research, which is describing the human proteome and its dynamic posttranslational modifications with unprecedented depth. Finally, we provide a perspective on studying proteomes at single-cell resolution. Expected final online publication date for the Annual Review of Genomics and Human Genetics, Volume 23 is October 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Collapse
Affiliation(s)
- Ana Martinez-Val
- Novo Nordisk Foundation Center for Protein Research, Proteomics Program, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark;
| | - Ulises H Guzmán
- Novo Nordisk Foundation Center for Protein Research, Proteomics Program, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark;
| | - Jesper V Olsen
- Novo Nordisk Foundation Center for Protein Research, Proteomics Program, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark;
| |
Collapse
|
24
|
Liu X, Rossio V, Thakurta SG, Flora A, Foster L, Bomgarden RD, Gygi SP, Paulo JA. Fe 3+-NTA magnetic beads as an alternative to spin column-based phosphopeptide enrichment. J Proteomics 2022; 260:104561. [PMID: 35331916 DOI: 10.1016/j.jprot.2022.104561] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/05/2022] [Accepted: 03/12/2022] [Indexed: 12/18/2022]
Abstract
Protein phosphorylation is a central mechanism of cellular signal transduction in living organisms. Phosphoproteomic studies systematically catalogue and characterize alterations in phosphorylation states across multiple cellular conditions and are often incorporated into global proteomics experiments. Previously, we found that spin column-based Fe3+-NTA enrichment integrated well with our workflow but remained a bottleneck for methods that require higher throughput or a scale that is beyond the capacity of these columns. Here, we compare our well-established spin column-based enrichment strategy with one encompassing magnetic beads. Our data show little difference when using either method in terms of the number of identified phosphopeptides as well as their physicochemical properties. In all, we illustrate how the potentially scalable and automation-friendly magnetic Fe3+-NTA beads can seamlessly substitute spin column-based Fe3+-NTA agarose beads for global phosphoproteome profiling. SIGNIFICANCE: Protein phosphorylation plays a key role in regulating a multitude of biological processes and can lead to insights into disease pathogenesis. Methodologies which can efficiently enrich phosphopeptides in a scalable and high-throughput manner are essential for profiling dynamic phosphoproteomes. Here we compare two phosphopeptide enrichment workflows, a well-established spin column-based strategy with agarose Fe3+-NTA beads and a strategy using magnetic Fe3+-NTA beads. Our data suggest that the scalable and automation-friendly magnetic bead-based workflow is an equivalent, but more flexible, enrichment strategy for phosphoproteome profiling experiments.
Collapse
Affiliation(s)
- Xinyue Liu
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Valentina Rossio
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | | | | | | | | | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.
| |
Collapse
|
25
|
Zhang W, Lai CK, Huang W, Li W, Wu S, Kong Q, Hopkinson AC, Fernie AR, Siu KWM, Yan S. An eco-friendly, low-cost, and automated strategy for phosphoproteome profiling. GREEN CHEMISTRY 2022; 24:9697-9708. [DOI: 10.1039/d2gc02345h] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/05/2024]
Abstract
An automated, online analysis platform using a reusable phos-trap column helps reduce organic solvent, plastic consumables, waste, and labor costs in phosphoproteomic studies.
Collapse
Affiliation(s)
- Wenyang Zhang
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Cheuk-Kuen Lai
- Department of Chemistry and Centre for Research in Mass Spectrometry, York University, Toronto, Ontario, M3J 1P3, Canada
| | - Wenjie Huang
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Wenyan Li
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Shaowen Wu
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Qian Kong
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Alan C. Hopkinson
- Department of Chemistry and Centre for Research in Mass Spectrometry, York University, Toronto, Ontario, M3J 1P3, Canada
| | - Alisdair R. Fernie
- Max Planck Institute of Molecular Plant Physiology, Am Muhlenberg 1, 14476, Potsdam-Golm, Germany
| | - K. W. Michael Siu
- Department of Chemistry and Centre for Research in Mass Spectrometry, York University, Toronto, Ontario, M3J 1P3, Canada
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario, N9B 3P4, Canada
| | - Shijuan Yan
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| |
Collapse
|
26
|
Bernardino RMM, Leão R, Henrique R, Pinheiro LC, Kumar P, Suravajhala P, Beck HC, Carvalho AS, Matthiesen R. Extracellular Vesicle Proteome in Prostate Cancer: A Comparative Analysis of Mass Spectrometry Studies. Int J Mol Sci 2021; 22:ijms222413605. [PMID: 34948404 PMCID: PMC8707426 DOI: 10.3390/ijms222413605] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/15/2021] [Accepted: 12/15/2021] [Indexed: 12/24/2022] Open
Abstract
Molecular diagnostics based on discovery research holds the promise of improving screening methods for prostate cancer (PCa). Furthermore, the congregated information prompts the question whether the urinary extracellular vesicles (uEV) proteome has been thoroughly explored, especially at the proteome level. In fact, most extracellular vesicles (EV) based biomarker studies have mainly targeted plasma or serum. Therefore, in this study, we aim to inquire about possible strategies for urinary biomarker discovery particularly focused on the proteome of urine EVs. Proteomics data deposited in the PRIDE archive were reanalyzed to target identifications of potential PCa markers. Network analysis of the markers proposed by different prostate cancer studies revealed moderate overlap. The recent throughput improvements in mass spectrometry together with the network analysis performed in this study, suggest that a larger standardized cohort may provide potential biomarkers that are able to fully characterize the heterogeneity of PCa. According to our analysis PCa studies based on urinary EV proteome presents higher protein coverage compared to plasma, plasma EV, and voided urine proteome. This together with a direct interaction of the prostate gland and urethra makes uEVs an attractive option for protein biomarker studies. In addition, urinary proteome based PCa studies must also evaluate samples from bladder and renal cancers to assess specificity for PCa.
Collapse
Affiliation(s)
- Rui Miguel Marques Bernardino
- Computational and Experimental Biology Group, Chronic Diseases Research Centre (CEDOC), NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, 1169-056 Lisboa, Portugal;
- Urology Department, Centro Hospitalar e Universitário de Lisboa Central, 1169-050 Lisbon, Portugal;
- Correspondence: (R.M.M.B.); (R.M.); Tel.: +351-939218696 (R.M.M.B. & R.M.)
| | - Ricardo Leão
- Faculty of Medicine, University of Coimbra, 3000-370 Coimbra, Portugal;
| | - Rui Henrique
- Pathology Department, Instituto Português de Oncologia, 4200-072 Porto, Portugal;
| | - Luis Campos Pinheiro
- Urology Department, Centro Hospitalar e Universitário de Lisboa Central, 1169-050 Lisbon, Portugal;
| | - Prashant Kumar
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, India;
- Somaiya Institute of Research and Consultancy (SIRAC), Somaiya Vidyavihar University (SVU), Vidyavihar, Mumbai 400077, India
| | - Prashanth Suravajhala
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Amritapuri Campus, Clappana P.O., Kollam 690525, India;
| | - Hans Christian Beck
- Centre for Clinical Proteomics, Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, 5000 Odense, Denmark;
| | - Ana Sofia Carvalho
- Computational and Experimental Biology Group, Chronic Diseases Research Centre (CEDOC), NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, 1169-056 Lisboa, Portugal;
| | - Rune Matthiesen
- Computational and Experimental Biology Group, Chronic Diseases Research Centre (CEDOC), NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, 1169-056 Lisboa, Portugal;
- Correspondence: (R.M.M.B.); (R.M.); Tel.: +351-939218696 (R.M.M.B. & R.M.)
| |
Collapse
|
27
|
Zhang W, Ren J, Lu J, Li P, Zhang W, Wang H, Tang B. Elucidating the Relationship between ROS and Protein Phosphorylation through In Situ Fluorescence Imaging in the Pneumonia Mice. Anal Chem 2021; 93:10907-10915. [PMID: 34324298 DOI: 10.1021/acs.analchem.1c01690] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Revealing the relationship between reactive oxygen species (ROS) and levels of protein phosphorylation is of great significance for understanding the pathogenesis of diseases. Although mass spectrometry is used as a classical method for protein phosphorylation analysis, there are still some challenges to realize in vivo protein phosphorylation recognition. Herein, we designed and prepared an metal-organic framework (MOF)-based fluorescent nanoprobe with Zr(IV) and boronate ester as an active center, which achieved simultaneous recognition of ROS and phosphorylation sites. The ROS unit was constructed by 1,8-naphthalimide and boronate ester as a fluorophore and a recognition group, respectively. The specific interaction between Zr(IV) and a phosphate group was used to realize fluorescence imaging of phosphorylation sites. Using the advantages of two-photon property of the ROS recognition unit, the nanoprobe can effectively reduce the background fluorescence and thus improve the imaging sensitivity. Finally, the MOF-based nanoprobe was successfully applied to reveal the relationship between ROS and levels of phosphorylation in pneumonia mice, which illustrated that the ROS and phosphorylation levels in the process of pulmonary inflammation were obviously higher than those of the normal mice. This work provides feasible fluorescence tools that have important significance for revealing pathogenesis of diseases.
Collapse
Affiliation(s)
- Wei Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Institute of Biomedical Sciences, Shandong Normal University, Jinan 250014, P. R. China
| | - Jie Ren
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Institute of Biomedical Sciences, Shandong Normal University, Jinan 250014, P. R. China
| | - Jun Lu
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Institute of Biomedical Sciences, Shandong Normal University, Jinan 250014, P. R. China
| | - Ping Li
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Institute of Biomedical Sciences, Shandong Normal University, Jinan 250014, P. R. China
| | - Wen Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Institute of Biomedical Sciences, Shandong Normal University, Jinan 250014, P. R. China
| | - Hui Wang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Institute of Biomedical Sciences, Shandong Normal University, Jinan 250014, P. R. China
| | - Bo Tang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Institute of Biomedical Sciences, Shandong Normal University, Jinan 250014, P. R. China
| |
Collapse
|
28
|
Dunphy K, Dowling P, Bazou D, O’Gorman P. Current Methods of Post-Translational Modification Analysis and Their Applications in Blood Cancers. Cancers (Basel) 2021; 13:1930. [PMID: 33923680 PMCID: PMC8072572 DOI: 10.3390/cancers13081930] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/04/2021] [Accepted: 04/14/2021] [Indexed: 12/12/2022] Open
Abstract
Post-translational modifications (PTMs) add a layer of complexity to the proteome through the addition of biochemical moieties to specific residues of proteins, altering their structure, function and/or localization. Mass spectrometry (MS)-based techniques are at the forefront of PTM analysis due to their ability to detect large numbers of modified proteins with a high level of sensitivity and specificity. The low stoichiometry of modified peptides means fractionation and enrichment techniques are often performed prior to MS to improve detection yields. Immuno-based techniques remain popular, with improvements in the quality of commercially available modification-specific antibodies facilitating the detection of modified proteins with high affinity. PTM-focused studies on blood cancers have provided information on altered cellular processes, including cell signaling, apoptosis and transcriptional regulation, that contribute to the malignant phenotype. Furthermore, the mechanism of action of many blood cancer therapies, such as kinase inhibitors, involves inhibiting or modulating protein modifications. Continued optimization of protocols and techniques for PTM analysis in blood cancer will undoubtedly lead to novel insights into mechanisms of malignant transformation, proliferation, and survival, in addition to the identification of novel biomarkers and therapeutic targets. This review discusses techniques used for PTM analysis and their applications in blood cancer research.
Collapse
Affiliation(s)
- Katie Dunphy
- Department of Biology, National University of Ireland, W23 F2K8 Maynooth, Ireland; (K.D.); (P.D.)
| | - Paul Dowling
- Department of Biology, National University of Ireland, W23 F2K8 Maynooth, Ireland; (K.D.); (P.D.)
| | - Despina Bazou
- Department of Haematology, Mater Misericordiae University Hospital, D07 WKW8 Dublin, Ireland;
| | - Peter O’Gorman
- Department of Haematology, Mater Misericordiae University Hospital, D07 WKW8 Dublin, Ireland;
| |
Collapse
|