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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. [PMID: 38806410 DOI: 10.1021/jasms.4c00147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [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.
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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
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2
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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).
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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.
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3
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Thiery J, Fahrner M. Integration of proteomics in the molecular tumor board. Proteomics 2023:e2300002. [PMID: 38143279 DOI: 10.1002/pmic.202300002] [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: 07/24/2023] [Revised: 12/03/2023] [Accepted: 12/05/2023] [Indexed: 12/26/2023]
Abstract
Cancer remains one of the most complex and challenging diseases in mankind. To address the need for a personalized treatment approach for particularly complex tumor cases, molecular tumor boards (MTBs) have been initiated. MTBs are interdisciplinary teams that perform in-depth molecular diagnostics to cooperatively and interdisciplinarily advise on the best therapeutic strategy. Current molecular diagnostics are routinely performed on the transcriptomic and genomic levels, aiming to identify tumor-driving mutations. However, these approaches can only partially capture the actual phenotype and the molecular key players of tumor growth and progression. Thus, direct investigation of the expressed proteins and activated signaling pathways provide valuable complementary information on the tumor-driving molecular characteristics of the tissue. Technological advancements in mass spectrometry-based proteomics enable the robust, rapid, and sensitive detection of thousands of proteins in minimal sample amounts, paving the way for clinical proteomics and the probing of oncogenic signaling activity. Therefore, proteomics is currently being integrated into molecular diagnostics within MTBs and holds promising potential in aiding tumor classification and identifying personalized treatment strategies. This review introduces MTBs and describes current clinical proteomics, its potential in precision oncology, and highlights the benefits of multi-omic data integration.
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Affiliation(s)
- Johanna Thiery
- Institute for Surgical Pathology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Matthias Fahrner
- Institute for Surgical Pathology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK) and Cancer Research Center (DKFZ), Freiburg, Germany
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4
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Gallo R, Rai AK, McIntyre ABR, Meyer K, Pelkmans L. DYRK3 enables secretory trafficking by maintaining the liquid-like state of ER exit sites. Dev Cell 2023; 58:1880-1897.e11. [PMID: 37643612 DOI: 10.1016/j.devcel.2023.08.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 02/16/2023] [Accepted: 08/01/2023] [Indexed: 08/31/2023]
Abstract
The dual-specificity kinase DYRK3 controls the formation and dissolution of multiple biomolecular condensates, regulating processes including stress recovery and mitotic progression. Here, we report that DYRK3 functionally interacts with proteins associated with endoplasmic reticulum (ER) exit sites (ERESs) and that inhibition of DYRK3 perturbs the organization of the ERES-Golgi interface and secretory trafficking. DYRK3-mediated regulation of ERES depends on the N-terminal intrinsically disordered region (IDR) of the peripheral membrane protein SEC16A, which co-phase separates with ERES components to form liquid-like condensates on the surface of the ER. By modulating the liquid-like properties of ERES, we show that their physical state is essential for functional cargo trafficking through the early secretory pathway. Our findings support a mechanism whereby phosphorylation by DYRK3 and its reversal by serine-threonine phosphatases regulate the material properties of ERES to create a favorable physicochemical environment for directional membrane traffic in eukaryotic cells.
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Affiliation(s)
- Raffaella Gallo
- Department of Molecular Life Sciences, University of Zurich, 8046 Zurich, Switzerland
| | - Arpan Kumar Rai
- Department of Molecular Life Sciences, University of Zurich, 8046 Zurich, Switzerland.
| | - Alexa B R McIntyre
- Department of Molecular Life Sciences, University of Zurich, 8046 Zurich, Switzerland
| | - Katrina Meyer
- Department of Molecular Life Sciences, University of Zurich, 8046 Zurich, Switzerland
| | - Lucas Pelkmans
- Department of Molecular Life Sciences, University of Zurich, 8046 Zurich, Switzerland.
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5
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Berber M, Leng S, Wengi A, Winter DV, Odermatt A, Beuschlein F, Loffing J, Breault DT, Penton D. Calcineurin regulates aldosterone production via dephosphorylation of NFATC4. JCI Insight 2023; 8:e157027. [PMID: 37310791 PMCID: PMC10443813 DOI: 10.1172/jci.insight.157027] [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: 01/18/2022] [Accepted: 06/08/2023] [Indexed: 06/15/2023] Open
Abstract
The mineralocorticoid aldosterone, secreted by the adrenal zona glomerulosa (ZG), is critical for life, maintaining ion homeostasis and blood pressure. Therapeutic inhibition of protein phosphatase 3 (calcineurin, Cn) results in inappropriately low plasma aldosterone levels despite concomitant hyperkalemia and hyperreninemia. We tested the hypothesis that Cn participates in the signal transduction pathway regulating aldosterone synthesis. Inhibition of Cn with tacrolimus abolished the potassium-stimulated (K+-stimulated) expression of aldosterone synthase, encoded by CYP11B2, in the NCI-H295R human adrenocortical cell line as well as ex vivo in mouse and human adrenal tissue. ZG-specific deletion of the regulatory Cn subunit CnB1 diminished Cyp11b2 expression in vivo and disrupted K+-mediated aldosterone synthesis. Phosphoproteomics analysis identified nuclear factor of activated T cells, cytoplasmic 4 (NFATC4), as a target for Cn-mediated dephosphorylation. Deletion of NFATC4 impaired K+-dependent stimulation of CYP11B2 expression and aldosterone production while expression of a constitutively active form of NFATC4 increased expression of CYP11B2 in NCI-H295R cells. Chromatin immunoprecipitation revealed NFATC4 directly regulated CYP11B2 expression. Thus, Cn controls aldosterone production via the Cn/NFATC4 pathway. Inhibition of Cn/NFATC4 signaling may explain low plasma aldosterone levels and hyperkalemia in patients treated with tacrolimus, and the Cn/NFATC4 pathway may provide novel molecular targets to treat primary aldosteronism.
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Affiliation(s)
- Mesut Berber
- Institute of Anatomy, University of Zurich, Switzerland
- Swiss National Centre for Competence in Research “Kidney Control of Homeostasis” (NCCR Kidney.CH), Zurich, Switzerland
| | - Sining Leng
- Department of Pediatrics, Harvard Medical School, Boston Children’s Hospital, Boston, Massachusetts, USA
- Division of Endocrinology, Boston Children’s Hospital, Boston, Massachusetts, USA
| | | | - Denise V. Winter
- Swiss Centre for Applied Human Toxicology and Division of Molecular and Systems Toxicology, Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland
| | - Alex Odermatt
- Swiss Centre for Applied Human Toxicology and Division of Molecular and Systems Toxicology, Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland
| | - Felix Beuschlein
- Swiss National Centre for Competence in Research “Kidney Control of Homeostasis” (NCCR Kidney.CH), Zurich, Switzerland
- Department of Endocrinology, Diabetology and Clinical Nutrition, University Hospital Zurich and University of Zurich, Zurich, Switzerland
- Medizinische Klinik und Poliklinik IV, Klinikum der Universität München, Munich, Germany
| | - Johannes Loffing
- Institute of Anatomy, University of Zurich, Switzerland
- Swiss National Centre for Competence in Research “Kidney Control of Homeostasis” (NCCR Kidney.CH), Zurich, Switzerland
| | - David T. Breault
- Department of Pediatrics, Harvard Medical School, Boston Children’s Hospital, Boston, Massachusetts, USA
- Harvard Stem Cell Institute, Cambridge, Massachusetts, USA
| | - David Penton
- Institute of Anatomy, University of Zurich, Switzerland
- Swiss National Centre for Competence in Research “Kidney Control of Homeostasis” (NCCR Kidney.CH), Zurich, Switzerland
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Chen Y, Zhao C, Guo H, Zou W, Zhang Z, Wei D, Lu H, Zhang L, Zhao Y. Wip1 inhibits neutrophil extracellular traps to promote abscess formation in mice by directly dephosphorylating Coronin-1a. Cell Mol Immunol 2023:10.1038/s41423-023-01057-2. [PMID: 37386173 PMCID: PMC10387484 DOI: 10.1038/s41423-023-01057-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 06/04/2023] [Indexed: 07/01/2023] Open
Abstract
Neutrophil extracellular traps (NETs) participate in the rapid inhibition and clearance of pathogens during infection; however, the molecular regulation of NET formation remains poorly understood. In the current study, we found that inhibition of the wild-type p53-induced phosphatase 1 (Wip1) significantly suppressed the activity of Staphylococcus aureus (S. aureus) and accelerated abscess healing in S. aureus-induced abscess model mice by enhancing NET formation. A Wip1 inhibitor significantly enhanced NET formation in mouse and human neutrophils in vitro. High-resolution mass spectrometry and biochemical assays demonstrated that Coro1a is a substrate of Wip1. Further experiments also revealed that Wip1 preferentially and directly interacts with phosphorylated Coro1a than compared to unphosphorylated inactivated Coro1a. The phosphorylated Ser426 site of Coro1a and the 28-90 aa domain of Wip1 are essential for the direct interaction of Coro1a and Wip1 and for Wip1 dephosphorylation of p-Coro1a Ser426. Wip1 deletion or inhibition in neutrophils significantly upregulated the phosphorylation of Coro1a-Ser426, which activated phospholipase C and subsequently the calcium pathway, the latter of which promoted NET formation after infection or lipopolysaccharide stimulation. This study revealed Coro1a to be a novel substrate of Wip1 and showed that Wip1 is a negative regulator of NET formation during infection. These results support the potential application of Wip1 inhibitors to treat bacterial infections.
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Affiliation(s)
- Yifang Chen
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regeneration, Beijing, China
| | - Chenxu Zhao
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Han Guo
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Weilong Zou
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, China
| | - Zhaoqi Zhang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Dong Wei
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Hezhe Lu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
- Beijing Institute for Stem Cell and Regeneration, Beijing, China.
| | - Lianfeng Zhang
- Key Laboratory of Human Diseases Comparative Medicine, Ministry of Health; Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Beijing, China.
| | - Yong Zhao
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
- Beijing Institute for Stem Cell and Regeneration, Beijing, China.
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
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7
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Hamza GM, Miele E, Wojchowski DM, Toran P, Worsfold CR, Anthonymuthu TS, Bergo VB, Zhang AX, Silva JC. Affi-BAMS™: A Robust Targeted Proteomics Microarray Platform to Measure Histone Post-Translational Modifications. Int J Mol Sci 2023; 24:10060. [PMID: 37373206 DOI: 10.3390/ijms241210060] [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: 05/25/2023] [Revised: 06/08/2023] [Accepted: 06/11/2023] [Indexed: 06/29/2023] Open
Abstract
For targeted protein panels, the ability to specifically assay post-translational modifications (PTMs) in a quantitative, sensitive, and straightforward manner would substantially advance biological and pharmacological studies. The present study highlights the effectiveness of the Affi-BAMS™ epitope-directed affinity bead capture/MALDI MS platform for quantitatively defining complex PTM marks of H3 and H4 histones. Using H3 and H4 histone peptides and isotopically labelled derivatives, this affinity bead and MALDI MS platform achieves a range of >3 orders of magnitude with a technical precision CV of <5%. Using nuclear cellular lysates, Affi-BAMS PTM-peptide capture resolves heterogeneous histone N-terminal PTMs with as little as 100 µg of starting material. In an HDAC inhibitor and MCF7 cell line model, the ability to monitor dynamic histone H3 acetylation and methylation events is further demonstrated (including SILAC quantification). Affi-BAMS (and its capacity for the multiplexing of samples and target PTM-proteins) thus provides a uniquely efficient and effective approach for analyzing dynamic epigenetic histone marks, which is critical for the regulation of chromatin structure and gene expression.
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Affiliation(s)
- Ghaith M Hamza
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Boston, MA 02451, USA
- Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA
| | - Eric Miele
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Boston, MA 02451, USA
| | - Don M Wojchowski
- Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA
| | - Paul Toran
- Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA
| | | | | | | | - Andrew X Zhang
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Boston, MA 02451, USA
| | - Jeffrey C Silva
- Adeptrix Corporation, Beverly, MA 01915, USA
- Cell Signaling Technology, Danvers, MA 01915, USA
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8
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Chang A, Leutert M, Rodriguez-Mias RA, Villén J. Automated Enrichment of Phosphotyrosine Peptides for High-Throughput Proteomics. J Proteome Res 2023; 22:1868-1880. [PMID: 37097255 PMCID: PMC10510590 DOI: 10.1021/acs.jproteome.2c00850] [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] [Indexed: 04/26/2023]
Abstract
Phosphotyrosine (pY) enrichment is critical for expanding the fundamental and clinical understanding of cellular signaling by mass spectrometry-based proteomics. However, current pY enrichment methods exhibit a high cost per sample and limited reproducibility due to expensive affinity reagents and manual processing. We present rapid-robotic phosphotyrosine proteomics (R2-pY), which uses a magnetic particle processor and pY superbinders or antibodies. R2-pY can handle up to 96 samples in parallel, requires 2 days to go from cell lysate to mass spectrometry injections, and results in global proteomic, phosphoproteomic, and tyrosine-specific phosphoproteomic samples. We benchmark the method on HeLa cells stimulated with pervanadate and serum and report over 4000 unique pY sites from 1 mg of peptide input, strong reproducibility between replicates, and phosphopeptide enrichment efficiencies above 99%. R2-pY extends our previously reported R2-P2 proteomic and global phosphoproteomic sample preparation framework, opening the door to large-scale studies of pY signaling in concert with global proteome and phosphoproteome profiling.
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Affiliation(s)
- Alexis Chang
- Department of Genome Sciences, University of Washington, Seattle WA 98195, USA
| | - Mario Leutert
- Department of Genome Sciences, University of Washington, Seattle WA 98195, USA
| | | | - Judit Villén
- Department of Genome Sciences, University of Washington, Seattle WA 98195, USA
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9
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Messner CB, Demichev V, Wang Z, Hartl J, Kustatscher G, Mülleder M, Ralser M. Mass spectrometry-based high-throughput proteomics and its role in biomedical studies and systems biology. Proteomics 2023; 23:e2200013. [PMID: 36349817 DOI: 10.1002/pmic.202200013] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 10/13/2022] [Accepted: 10/13/2022] [Indexed: 11/11/2022]
Abstract
There are multiple reasons why the next generation of biological and medical studies require increasing numbers of samples. Biological systems are dynamic, and the effect of a perturbation depends on the genetic background and environment. As a consequence, many conditions need to be considered to reach generalizable conclusions. Moreover, human population and clinical studies only reach sufficient statistical power if conducted at scale and with precise measurement methods. Finally, many proteins remain without sufficient functional annotations, because they have not been systematically studied under a broad range of conditions. In this review, we discuss the latest technical developments in mass spectrometry (MS)-based proteomics that facilitate large-scale studies by fast and efficient chromatography, fast scanning mass spectrometers, data-independent acquisition (DIA), and new software. We further highlight recent studies which demonstrate how high-throughput (HT) proteomics can be applied to capture biological diversity, to annotate gene functions or to generate predictive and prognostic models for human diseases.
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Affiliation(s)
- Christoph B Messner
- Precision Proteomics Center, Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
| | - Vadim Demichev
- Institute of Biochemistry, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Ziyue Wang
- Institute of Biochemistry, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Johannes Hartl
- Institute of Biochemistry, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Georg Kustatscher
- Wellcome Centre for Cell Biology, University of Edinburgh, Max Born Crescent, Edinburgh, Scotland, UK
| | - Michael Mülleder
- Core Facility High Throughput Mass Spectrometry, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Markus Ralser
- Institute of Biochemistry, Charité - Universitätsmedizin Berlin, Berlin, Germany
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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10
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Peng C, Li S, Wang Y, Ge L, Zhang S, Cai Q, Zhen D, Chen P. Preparation of Er-Nd-TiO2 nanocomposite for the highly selective enrichment of phosphotyrosine peptides. Microchem J 2023. [DOI: 10.1016/j.microc.2023.108597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
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11
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Gray AL, Karlsson R, Roberts ARE, Ridley AJL, Pun N, Khan B, Lawless C, Luís R, Szpakowska M, Chevigné A, Hughes CE, Medina-Ruiz L, Birchenough HL, Mulholland IZ, Salanga CL, Yates EA, Turnbull JE, Handel TM, Graham GJ, Jowitt TA, Schiessl I, Richter RP, Miller RL, Dyer DP. Chemokine CXCL4 interactions with extracellular matrix proteoglycans mediate widespread immune cell recruitment independent of chemokine receptors. Cell Rep 2023; 42:111930. [PMID: 36640356 PMCID: PMC11064100 DOI: 10.1016/j.celrep.2022.111930] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 11/18/2022] [Accepted: 12/14/2022] [Indexed: 01/07/2023] Open
Abstract
Leukocyte recruitment from the vasculature into tissues is a crucial component of the immune system but is also key to inflammatory disease. Chemokines are central to this process but have yet to be therapeutically targeted during inflammation due to a lack of mechanistic understanding. Specifically, CXCL4 (Platelet Factor 4, PF4) has no established receptor that explains its function. Here, we use biophysical, in vitro, and in vivo techniques to determine the mechanism underlying CXCL4-mediated leukocyte recruitment. We demonstrate that CXCL4 binds to glycosaminoglycan (GAG) sugars on proteoglycans within the endothelial extracellular matrix, resulting in increased adhesion of leukocytes to the vasculature, increased vascular permeability, and non-specific recruitment of a range of leukocytes. Furthermore, GAG sulfation confers selectivity onto chemokine localization. These findings present mechanistic insights into chemokine biology and provide future therapeutic targets.
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Affiliation(s)
- Anna L Gray
- Wellcome Centre for Cell-Matrix Research, Lydia Becker Institute of Immunology and Inflammation, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK; Geoffrey Jefferson Brain Research Centre, Manchester Academic Health Science Centre, Northern Care Alliance NHS Group, University of Manchester, Manchester, UK
| | - Richard Karlsson
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen, Denmark
| | - Abigail R E Roberts
- University of Leeds, School of Biomedical Sciences, Faculty of Biological Sciences, School of Physics and Astronomy, Faculty of Engineering and Physical Sciences, Astbury Centre for Structural Molecular Biology, and Bragg Centre for Materials Research, Leeds LS2 9JT, UK
| | - Amanda J L Ridley
- Wellcome Centre for Cell-Matrix Research, Lydia Becker Institute of Immunology and Inflammation, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Nabina Pun
- Wellcome Centre for Cell-Matrix Research, Lydia Becker Institute of Immunology and Inflammation, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Bakhtbilland Khan
- Wellcome Centre for Cell-Matrix Research, Lydia Becker Institute of Immunology and Inflammation, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Craig Lawless
- Wellcome Centre for Cell-Matrix Research, Lydia Becker Institute of Immunology and Inflammation, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Rafael Luís
- Immuno-Pharmacology and Interactomics, Department of Infection and Immunity, Luxembourg Institute of Health, 4354 Esch-sur-Alzette, Luxembourg; Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg; Tumor Immunotherapy and Microenvironment, Department of Cancer Research, Luxembourg Institute of Health, 2012 Luxembourg, Luxembourg
| | - Martyna Szpakowska
- Immuno-Pharmacology and Interactomics, Department of Infection and Immunity, Luxembourg Institute of Health, 4354 Esch-sur-Alzette, Luxembourg
| | - Andy Chevigné
- Immuno-Pharmacology and Interactomics, Department of Infection and Immunity, Luxembourg Institute of Health, 4354 Esch-sur-Alzette, Luxembourg
| | - Catherine E Hughes
- Chemokine Research Group, School of Infection and Immunity, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, UK
| | - Laura Medina-Ruiz
- Chemokine Research Group, School of Infection and Immunity, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, UK
| | - Holly L Birchenough
- Wellcome Centre for Cell-Matrix Research, Lydia Becker Institute of Immunology and Inflammation, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Iashia Z Mulholland
- Wellcome Centre for Cell-Matrix Research, Lydia Becker Institute of Immunology and Inflammation, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Catherina L Salanga
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Edwin A Yates
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Jeremy E Turnbull
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen, Denmark; Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK; Centre for Glycosciences, Keele University, Keele, Staffordshire ST5 5BG, UK
| | - Tracy M Handel
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Gerard J Graham
- Chemokine Research Group, School of Infection and Immunity, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, UK
| | - Thomas A Jowitt
- Wellcome Centre for Cell-Matrix Research, Lydia Becker Institute of Immunology and Inflammation, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Ingo Schiessl
- Geoffrey Jefferson Brain Research Centre, Manchester Academic Health Science Centre, Northern Care Alliance NHS Group, University of Manchester, Manchester, UK; Division of Neuroscience, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Ralf P Richter
- University of Leeds, School of Biomedical Sciences, Faculty of Biological Sciences, School of Physics and Astronomy, Faculty of Engineering and Physical Sciences, Astbury Centre for Structural Molecular Biology, and Bragg Centre for Materials Research, Leeds LS2 9JT, UK
| | - Rebecca L Miller
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen, Denmark
| | - Douglas P Dyer
- Wellcome Centre for Cell-Matrix Research, Lydia Becker Institute of Immunology and Inflammation, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK; Geoffrey Jefferson Brain Research Centre, Manchester Academic Health Science Centre, Northern Care Alliance NHS Group, University of Manchester, Manchester, UK.
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12
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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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13
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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]
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14
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A Non-Hazardous Deparaffinization Protocol Enables Quantitative Proteomics of Core Needle Biopsy-Sized Formalin-Fixed and Paraffin-Embedded (FFPE) Tissue Specimens. Int J Mol Sci 2022; 23:ijms23084443. [PMID: 35457260 PMCID: PMC9031572 DOI: 10.3390/ijms23084443] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/09/2022] [Accepted: 04/11/2022] [Indexed: 12/22/2022] Open
Abstract
Most human tumor tissues that are obtained for pathology and diagnostic purposes are formalin-fixed and paraffin-embedded (FFPE). To perform quantitative proteomics of FFPE samples, paraffin has to be removed and formalin-induced crosslinks have to be reversed prior to proteolytic digestion. A central component of almost all deparaffinization protocols is xylene, a toxic and highly flammable solvent that has been reported to negatively affect protein extraction and quantitative proteome analysis. Here, we present a 'green' xylene-free protocol for accelerated sample preparation of FFPE tissues based on paraffin-removal with hot water. Combined with tissue homogenization using disposable micropestles and a modified protein aggregation capture (PAC) digestion protocol, our workflow enables streamlined and reproducible quantitative proteomic profiling of FFPE tissue. Label-free quantitation of FFPE cores from human ductal breast carcinoma in situ (DCIS) xenografts with a volume of only 0.79 mm3 showed a high correlation between replicates (r2 = 0.992) with a median %CV of 16.9%. Importantly, this small volume is already compatible with tissue micro array (TMA) cores and core needle biopsies, while our results and its ease-of-use indicate that further downsizing is feasible. Finally, our FFPE workflow does not require costly equipment and can be established in every standard clinical laboratory.
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15
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Hunziker A, Stertz S. Unraveling virus-induced cellular signaling cascades by label-free quantitative phosphoproteomics. STAR Protoc 2022; 3:101089. [PMID: 35535160 PMCID: PMC9076958 DOI: 10.1016/j.xpro.2021.101089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Due to the low stoichiometry and highly transient nature of protein phosphorylation it is challenging to capture the dynamics and complexity of phosphorylation events on a systems level. Here, we present an optimized protocol to measure virus-induced phosphorylation events with high sensitivity using label free quantification-based phosphoproteomics. Specifically, we describe filter assisted protein digestion (FASP), enrichment of phosphopeptides, mass spectrometry, and subsequent bioinformatic analysis. For complete details on the use and execution of this protocol, please refer to Hunziker et al. (2022).
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Affiliation(s)
- Annika Hunziker
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
- Life Sciences Zurich Graduate School, ETH and University of Zurich, 8057 Zurich, Switzerland
| | - Silke Stertz
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
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16
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Wu Y, Chen H, Chen Y, Sun N, Deng C. Metal organic frameworks as advanced extraction adsorbents for separation and analysis in proteomics and environmental research. Sci China Chem 2022. [DOI: 10.1007/s11426-021-1195-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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17
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Hunziker A, Glas I, Pohl MO, Stertz S. Phosphoproteomic profiling of influenza virus entry reveals infection-triggered filopodia induction counteracted by dynamic cortactin phosphorylation. Cell Rep 2022; 38:110306. [DOI: 10.1016/j.celrep.2022.110306] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 11/19/2021] [Accepted: 01/06/2022] [Indexed: 11/03/2022] Open
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18
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Lee BY, Hogg EKJ, Below CR, Kononov A, Blanco-Gomez A, Heider F, Xu J, Hutton C, Zhang X, Scheidt T, Beattie K, Lamarca A, McNamara M, Valle JW, Jørgensen C. Heterocellular OSM-OSMR signalling reprograms fibroblasts to promote pancreatic cancer growth and metastasis. Nat Commun 2021; 12:7336. [PMID: 34921158 PMCID: PMC8683436 DOI: 10.1038/s41467-021-27607-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 11/22/2021] [Indexed: 12/13/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDA) is a lethal malignancy with a complex microenvironment. Dichotomous tumour-promoting and -restrictive roles have been ascribed to the tumour microenvironment, however the effects of individual stromal subsets remain incompletely characterised. Here, we describe how heterocellular Oncostatin M (OSM) - Oncostatin M Receptor (OSMR) signalling reprograms fibroblasts, regulates tumour growth and metastasis. Macrophage-secreted OSM stimulates inflammatory gene expression in cancer-associated fibroblasts (CAFs), which in turn induce a pro-tumourigenic environment and engage tumour cell survival and migratory signalling pathways. Tumour cells implanted in Osm-deficient (Osm-/-) mice display an epithelial-dominated morphology, reduced tumour growth and do not metastasise. Moreover, the tumour microenvironment of Osm-/- animals exhibit increased abundance of α smooth muscle actin positive myofibroblasts and a shift in myeloid and T cell phenotypes, consistent with a more immunogenic environment. Taken together, these data demonstrate how OSM-OSMR signalling coordinates heterocellular interactions to drive a pro-tumourigenic environment in PDA.
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Affiliation(s)
- Brian Y Lee
- Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park, SK10 4TG, Manchester, UK
| | - Elizabeth K J Hogg
- Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park, SK10 4TG, Manchester, UK
| | - Christopher R Below
- Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park, SK10 4TG, Manchester, UK
| | - Alexander Kononov
- Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park, SK10 4TG, Manchester, UK
| | - Adrian Blanco-Gomez
- Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park, SK10 4TG, Manchester, UK
| | - Felix Heider
- Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park, SK10 4TG, Manchester, UK
| | - Jingshu Xu
- Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park, SK10 4TG, Manchester, UK
| | - Colin Hutton
- Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park, SK10 4TG, Manchester, UK
| | - Xiaohong Zhang
- Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park, SK10 4TG, Manchester, UK
| | - Tamara Scheidt
- Department of Molecular Biology, University of Salzburg, Salzburg, Austria
| | - Kenneth Beattie
- FingerPrints Proteomics Facility, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Angela Lamarca
- Department of Medical Oncology, The Christie NHS Foundation Trust, Wilmslow Road, M20 4BX, Manchester, UK
- Institute of Cancer Sciences, University of Manchester, Wilmslow Road, M20 4BX, Manchester, UK
| | - Mairéad McNamara
- Department of Medical Oncology, The Christie NHS Foundation Trust, Wilmslow Road, M20 4BX, Manchester, UK
- Institute of Cancer Sciences, University of Manchester, Wilmslow Road, M20 4BX, Manchester, UK
| | - Juan W Valle
- Department of Medical Oncology, The Christie NHS Foundation Trust, Wilmslow Road, M20 4BX, Manchester, UK
- Institute of Cancer Sciences, University of Manchester, Wilmslow Road, M20 4BX, Manchester, UK
| | - Claus Jørgensen
- Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park, SK10 4TG, Manchester, UK.
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19
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Chen Y, Alba M, Tieu T, Tong Z, Minhas RS, Rudd D, Voelcker NH, Cifuentes-Rius A, Elnathan R. Engineering Micro–Nanomaterials for Biomedical Translation. ADVANCED NANOBIOMED RESEARCH 2021. [DOI: 10.1002/anbr.202100002] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
- Yaping Chen
- Monash Institute of Pharmaceutical Sciences Monash University 381 Royal Parade Parkville VIC 3052 Australia
- Melbourne Centre for Nanofabrication Victorian Node of the Australian National Fabrication Facility 151 Wellington Road Clayton VIC 3168 Australia
| | - Maria Alba
- Monash Institute of Pharmaceutical Sciences Monash University 381 Royal Parade Parkville VIC 3052 Australia
- Melbourne Centre for Nanofabrication Victorian Node of the Australian National Fabrication Facility 151 Wellington Road Clayton VIC 3168 Australia
| | - Terence Tieu
- Monash Institute of Pharmaceutical Sciences Monash University 381 Royal Parade Parkville VIC 3052 Australia
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Manufacturing Commonwealth Scientific and Industrial Research Organisation (CSIRO) Clayton VIC 3168 Australia
| | - Ziqiu Tong
- Monash Institute of Pharmaceutical Sciences Monash University 381 Royal Parade Parkville VIC 3052 Australia
| | - Rajpreet Singh Minhas
- Monash Institute of Pharmaceutical Sciences Monash University 381 Royal Parade Parkville VIC 3052 Australia
- Melbourne Centre for Nanofabrication Victorian Node of the Australian National Fabrication Facility 151 Wellington Road Clayton VIC 3168 Australia
| | - David Rudd
- Monash Institute of Pharmaceutical Sciences Monash University 381 Royal Parade Parkville VIC 3052 Australia
- Melbourne Centre for Nanofabrication Victorian Node of the Australian National Fabrication Facility 151 Wellington Road Clayton VIC 3168 Australia
| | - Nicolas H. Voelcker
- Monash Institute of Pharmaceutical Sciences Monash University 381 Royal Parade Parkville VIC 3052 Australia
- Melbourne Centre for Nanofabrication Victorian Node of the Australian National Fabrication Facility 151 Wellington Road Clayton VIC 3168 Australia
- Department of Materials Science and Engineering Monash University 22 Alliance Lane Clayton VIC 3168 Australia
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Manufacturing Commonwealth Scientific and Industrial Research Organisation (CSIRO) Clayton VIC 3168 Australia
- INM-Leibniz Institute for New Materials Campus D2 2 Saarbrücken 66123 Germany
| | - Anna Cifuentes-Rius
- Monash Institute of Pharmaceutical Sciences Monash University 381 Royal Parade Parkville VIC 3052 Australia
| | - Roey Elnathan
- Monash Institute of Pharmaceutical Sciences Monash University 381 Royal Parade Parkville VIC 3052 Australia
- Melbourne Centre for Nanofabrication Victorian Node of the Australian National Fabrication Facility 151 Wellington Road Clayton VIC 3168 Australia
- Department of Materials Science and Engineering Monash University 22 Alliance Lane Clayton VIC 3168 Australia
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20
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Wang X, Yu J, Yang H, Shen J, Liu H, Zhou J. A new Ti-based IMAC nanohybrid with high hydrophilicity and enhanced absorption capacity for the selective enrichment of phosphopeptides. J Chromatogr B Analyt Technol Biomed Life Sci 2021; 1179:122851. [PMID: 34246169 DOI: 10.1016/j.jchromb.2021.122851] [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: 01/05/2021] [Revised: 05/24/2021] [Accepted: 06/27/2021] [Indexed: 11/17/2022]
Abstract
Ti-based immobilized metal affinity chromatography (IMAC) nanomaterial has shown high potential in phosphoproteome mass-spectrometric (MS) analysis. However, the limited surface area and poor solubility will greatly restrict its use in phosphoproteome research. To overcome these two key drawbacks, a novel Ti-based IMAC nanomaterial was prepared by Ti-bonded β-cyclodextrin (β-CD) anchored on the surface of carbon nanotubes (CNTs) (denoted as COOH-CNTs-CD-Ti) and successfully applied as a biofunctional adsorbent for selectively enriching trace phosphopeptides. In the selective enrichment process, CNTs provided greater surface area for the absorption of phosphopeptides, while β-CD also offered a greater opportunity for the interaction between phosphopeptides and Ti4+. COOH-CNTs-CD-Ti with the aforementioned properities exhibited higher selectivity for phosphopeptides from the standard protein digests, the tryptic digests of nonfat milk and human serum, showing a great selective enrichment capability towards complex biological samples.
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Affiliation(s)
- XinHui Wang
- College of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China; College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - JiaLin Yu
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - HaoDing Yang
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Jian Shen
- College of Chemistry and Materials Science, Jiangsu Key Laboratory of Biofunctional Materials, Nanjing Normal University, Nanjing 210023, China
| | - HaiLong Liu
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China.
| | - JiaHong Zhou
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China.
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21
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Martinez-Fabregas J, Pohler E, Moraga I. Identifying cytokine signaling signatures in primary human Th-1 cells by phospho-proteomics analysis. STAR Protoc 2021; 2:100417. [PMID: 33870224 PMCID: PMC8044715 DOI: 10.1016/j.xpro.2021.100417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Stable isotope labeling by amino acid-based high-resolution phosphoproteomics is a powerful technique that allows for direct comparison of cells stimulated under different experimental conditions. This feature makes it the ideal methodology to identify cytokine signaling networks. Here, we present an optimized protocol for the isolation and identification of phosphopeptides from IL-6-stimulated primary human Th-1 cells. For complete details on the use and execution of this protocol, please refer to Martinez-Fabregas et al. (2020). Phosphoproteomics protocol for studying cytokines signaling in immune cells Tips for the isolation and expansion of primary human Th-1 cells Detailed protocol for the efficient SILAC labelling of human Th-1 cells
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Affiliation(s)
- Jonathan Martinez-Fabregas
- Division of Cell Signaling and Immunology, School of Life Sciences, University of Dundee, Dundee, UK
- Corresponding author
| | - Elizabeth Pohler
- Division of Cell Signaling and Immunology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Ignacio Moraga
- Division of Cell Signaling and Immunology, School of Life Sciences, University of Dundee, Dundee, UK
- Corresponding author
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22
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He Z, Zou T, Xiao Q, Yuan G, Liu M, Tao Y, Zhou D, Zhang X, Deng Q, Wang S, Zheng A, Zhu J, Liang Y, Yu X, Wang A, Liu H, Wang L, Li P, Li S. An L-type lectin receptor-like kinase promotes starch accumulation during rice pollen maturation. Development 2021; 148:dev.196378. [PMID: 33658224 DOI: 10.1242/dev.196378] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 02/22/2021] [Indexed: 01/27/2023]
Abstract
Starch accumulation is key for the maturity of rice pollen grains; however, the regulatory mechanism underlying this process remains unknown. Here, we have isolated a male-sterile rice mutant, abnormal pollen 1 (ap1), which produces nonviable pollen grains with defective starch accumulation. Functional analysis revealed that AP1 encodes an active L-type lectin receptor-like kinase (L-LecRLK). AP1 is localized to the plasma membrane and its transcript is highly accumulated in pollen during the starch synthesis phase. RNA-seq and phosphoproteomic analysis revealed that the expression/phosphorylation levels of numerous genes/proteins involved in starch and sucrose metabolism pathway were significantly altered in the mutant pollen, including a known rice UDP-glucose pyrophosphorylase (OsUGP2). We further found that AP1 physically interacts with OsUGP2 to elevate its enzymatic activity, likely through targeted phosphorylation. These findings revealed a novel role of L-LecRLK in controlling pollen maturity via modulating sucrose and starch metabolism.
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Affiliation(s)
- Zhiyuan He
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Ting Zou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Qiao Xiao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Guoqiang Yuan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Miaomiao Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Yang Tao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Dan Zhou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Xu Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Qiming Deng
- State Key Laboratory of Hybrid Rice, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Shiquan Wang
- State Key Laboratory of Hybrid Rice, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Aiping Zheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Jun Zhu
- State Key Laboratory of Hybrid Rice, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Yueyang Liang
- State Key Laboratory of Hybrid Rice, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiumei Yu
- State Key Laboratory of Hybrid Rice, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Aijun Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Huainian Liu
- State Key Laboratory of Hybrid Rice, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Lingxia Wang
- State Key Laboratory of Hybrid Rice, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Ping Li
- State Key Laboratory of Hybrid Rice, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Shuangcheng Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
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23
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Xiao J, Yang SS, Wu JX, Wu N, Yu X, Shang W, Gu ZY. Sn-based metal-organic framework for highly selective capture of monophosphopeptides. Talanta 2021; 224:121812. [PMID: 33379037 DOI: 10.1016/j.talanta.2020.121812] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 10/19/2020] [Accepted: 10/23/2020] [Indexed: 11/28/2022]
Abstract
Sn-based metal-organic framework (MOF) was utilized to effectively capture monophosphopeptides due to the unique affinity. The Sn-based MOF demonstrated the good sensitivity and selectivity in the model phosphoproteins enrichment and was successfully applied in the biological fluids.
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Affiliation(s)
- Jing Xiao
- Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, China
| | - Shi-Shu Yang
- Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, China
| | - Jian-Xiang Wu
- Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, China
| | - Nan Wu
- Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, China
| | - Xizhong Yu
- Key Laboratory for Metabolic Diseases in Chinese Medicine, First College of Clinical Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Wenbin Shang
- Key Laboratory for Metabolic Diseases in Chinese Medicine, First College of Clinical Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Zhi-Yuan Gu
- Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, China.
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24
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Zheng H, Zhang J, Ma J, Jia Q. Engineering Magnetic Guanidyl-Functionalized Supramolecular Organic Framework for Efficient Enrichment of Global Phosphopeptides. ACS APPLIED MATERIALS & INTERFACES 2020; 12:57468-57476. [PMID: 33295748 DOI: 10.1021/acsami.0c18803] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Comprehensive mass spectrometry-based proteomics analysis is currently available but remains challenging, especially for post-translational modifications of phosphorylated proteins. Herein, multifunctional magnetic pillar[5]arene supramolecular organic frameworks were fabricated and immobilized with arginine (mP5SOF-Arg) for highly effective enrichment of global phosphopeptides. The specific phosphate-P5/phosphate-guanidine affinities and large surface area with regular porosity contribute to the high enrichment capacity. By coupling with mass spectrometry, high detection sensitivity (0.1 fmol), excellent selectivity (1:5000 molar ratios of β-casein/cytochrome c), and high recyclability (seven cycles) were achieved for phosphopeptide analysis. mP5SOF-Arg can efficiently enrich phosphopeptides from practical samples, including defatted milk, egg yolk, and human saliva. Notably, a total of 450 phosphopeptides were explored for highly selective identification from A594 cells and 1445 phosphopeptides were identified from mouse liver tissue samples. mP5SOF-Arg exhibited great potential to serve as the basis for peptidomic research to identify phosphopeptides and provided insight for biomarker discovery.
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Affiliation(s)
- Haijiao Zheng
- College of Chemistry, Jilin University, Changchun 130012, China
| | - Jingchun Zhang
- China-Japan Union Hospital, Jilin University, Changchun 130033, China
| | - Jiutong Ma
- College of Chemistry, Jilin University, Changchun 130012, China
| | - Qiong Jia
- College of Chemistry, Jilin University, Changchun 130012, China
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25
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Arribas Diez I, Govender I, Naicker P, Stoychev S, Jordaan J, Jensen ON. Zirconium(IV)-IMAC Revisited: Improved Performance and Phosphoproteome Coverage by Magnetic Microparticles for Phosphopeptide Affinity Enrichment. J Proteome Res 2020; 20:453-462. [PMID: 33226818 DOI: 10.1021/acs.jproteome.0c00508] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Phosphopeptide enrichment is an essential step in large-scale, quantitative phosphoproteomics by mass spectrometry. Several phosphopeptide affinity enrichment techniques exist, such as immobilized metal-ion affinity chromatography (IMAC) and metal oxide affinity chromatography (MOAC). We compared zirconium(IV) IMAC (Zr-IMAC) magnetic microparticles to more commonly used titanium(IV) IMAC (Ti-IMAC) and TiO2 magnetic microparticles for phosphopeptide enrichment from simple and complex protein samples prior to phosphopeptide sequencing and characterization by mass spectrometry (liquid chromatography-tandem mass spectrometry, LC-MS/MS). We optimized sample-loading conditions to increase phosphopeptide recovery for Zr-IMAC-, Ti-IMAC-, and TiO2-based workflows by 22, 24, and 35%, respectively. The optimized protocol resulted in improved performance of Zr-IMAC over Ti-IMAC and TiO2 as well as high-performance liquid chromatography-based Fe(III)-IMAC with up to 23% more identified phosphopeptides. The different enrichment chemistries showed a high degree of overlap but also differences in phosphopeptide selectivity and complementarity. We conclude that Zr-IMAC improves phosphoproteome coverage and recommend that this complementary and scalable affinity enrichment method is more widely used in biological and biomedical studies of cell signaling and the search for biomarkers. Data are available via ProteomeXchange with identifier PXD018273.
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Affiliation(s)
- Ignacio Arribas Diez
- Department of Biochemistry & Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense M DK-5230, Denmark
| | - Ireshyn Govender
- NextGen Health, Council for Scientific and Industrial Research, Pretoria 0184, South Africa
| | - Previn Naicker
- NextGen Health, Council for Scientific and Industrial Research, Pretoria 0184, South Africa
| | - Stoyan Stoychev
- NextGen Health, Council for Scientific and Industrial Research, Pretoria 0184, South Africa.,ReSyn Biosciences, Pretoria 1610, Gauteng, South Africa
| | - Justin Jordaan
- ReSyn Biosciences, Pretoria 1610, Gauteng, South Africa.,Rhodes University, Grahamstown 6139, South Africa
| | - Ole N Jensen
- Department of Biochemistry & Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense M DK-5230, Denmark
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26
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Hoopmann MR, Kusebauch U, Palmblad M, Bandeira N, Shteynberg DD, He L, Xia B, Stoychev SH, Omenn GS, Weintraub ST, Moritz RL. Insights from the First Phosphopeptide Challenge of the MS Resource Pillar of the HUPO Human Proteome Project. J Proteome Res 2020; 19:4754-4765. [PMID: 33166149 DOI: 10.1021/acs.jproteome.0c00648] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Mass spectrometry has greatly improved the analysis of phosphorylation events in complex biological systems and on a large scale. Despite considerable progress, the correct identification of phosphorylated sites, their quantification, and their interpretation regarding physiological relevance remain challenging. The MS Resource Pillar of the Human Proteome Organization (HUPO) Human Proteome Project (HPP) initiated the Phosphopeptide Challenge as a resource to help the community evaluate methods, learn procedures and data analysis routines, and establish their own workflows by comparing results obtained from a standard set of 94 phosphopeptides (serine, threonine, tyrosine) and their nonphosphorylated counterparts mixed at different ratios in a neat sample and a yeast background. Participants analyzed both samples with their method(s) of choice to report the identification and site localization of these peptides, determine their relative abundances, and enrich for the phosphorylated peptides in the yeast background. We discuss the results from 22 laboratories that used a range of different methods, instruments, and analysis software. We reanalyzed submitted data with a single software pipeline and highlight the successes and challenges in correct phosphosite localization. All of the data from this collaborative endeavor are shared as a resource to encourage the development of even better methods and tools for diverse phosphoproteomic applications. All submitted data and search results were uploaded to MassIVE (https://massive.ucsd.edu/) as data set MSV000085932 with ProteomeXchange identifier PXD020801.
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Affiliation(s)
| | - Ulrike Kusebauch
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Magnus Palmblad
- Center for Proteomics and Metabolomics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Nuno Bandeira
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California 92093, United States
| | | | - Lingjie He
- Synpeptide Co., Ltd., Shanghai 201204, China
| | - Bin Xia
- Synpeptide Co., Ltd., Shanghai 201204, China
| | | | - Gilbert S Omenn
- Institute for Systems Biology, Seattle, Washington 98109, United States.,Departments of Computational Medicine and Bioinformatics, Internal Medicine, and Human Genetics and School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Susan T Weintraub
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, United States
| | - Robert L Moritz
- Institute for Systems Biology, Seattle, Washington 98109, United States
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27
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Alexovič M, Urban PL, Tabani H, Sabo J. Recent advances in robotic protein sample preparation for clinical analysis and other biomedical applications. Clin Chim Acta 2020; 507:104-116. [PMID: 32305536 DOI: 10.1016/j.cca.2020.04.015] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 04/11/2020] [Accepted: 04/13/2020] [Indexed: 02/06/2023]
Abstract
Discovery of new protein biomarker candidates has become a major research goal in the areas of clinical chemistry, analytical chemistry, and biomedicine. These important species constitute the molecular target when it comes to diagnosis, prognosis, and further monitoring of disease. However, their analysis requires powerful, selective and high-throughput sample preparation and product (analyte) characterisation approaches. In general, manual sample processing is tedious, complex and time-consuming, especially when large numbers of samples have to be processed (e.g., in clinical studies). Automation via microtiter-plate platforms involving robotics has brought improvements in high-throughput performance while comparable or even better precisions and repeatability (intra-day, inter-day) were achieved. At the same time, waste production and exposure of laboratory personnel to hazards were reduced. In comprehensive protein analysis workflows (e.g., liquid chromatography-tandem mass spectrometry analysis), sample preparation is an unavoidable step. This review surveys the recent achievements in automation of bottom-up and top-down protein and/or proteomics approaches. Emphasis is put on high-end multi-well plate robotic platforms developed for clinical analysis and other biomedical applications. The literature from 2013 to date has been covered.
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Affiliation(s)
- Michal Alexovič
- Department of Medical and Clinical Biophysics, Faculty of Medicine, University of P.J. Šafárik in Košice, 04011 Košice, Slovakia.
| | - Pawel L Urban
- Department of Chemistry, National Tsing Hua University, 101, Sec 2, Kuang-Fu Rd., Hsinchu 30013, Taiwan
| | - Hadi Tabani
- Department of Environmental Geology, Research Institute of Applied Sciences (ACECR), Shahid Beheshti University, Tehran, Iran
| | - Ján Sabo
- Department of Medical and Clinical Biophysics, Faculty of Medicine, University of P.J. Šafárik in Košice, 04011 Košice, Slovakia
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28
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Bekker-Jensen DB, Martínez-Val A, Steigerwald S, Rüther P, Fort KL, Arrey TN, Harder A, Makarov A, Olsen JV. A Compact Quadrupole-Orbitrap Mass Spectrometer with FAIMS Interface Improves Proteome Coverage in Short LC Gradients. Mol Cell Proteomics 2020; 19:716-729. [PMID: 32051234 PMCID: PMC7124470 DOI: 10.1074/mcp.tir119.001906] [Citation(s) in RCA: 199] [Impact Index Per Article: 49.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 02/03/2020] [Indexed: 12/31/2022] Open
Abstract
State-of-the-art proteomics-grade mass spectrometers can measure peptide precursors and their fragments with ppm mass accuracy at sequencing speeds of tens of peptides per second with attomolar sensitivity. Here we describe a compact and robust quadrupole-orbitrap mass spectrometer equipped with a front-end High Field Asymmetric Waveform Ion Mobility Spectrometry (FAIMS) Interface. The performance of the Orbitrap Exploris 480 mass spectrometer is evaluated in data-dependent acquisition (DDA) and data-independent acquisition (DIA) modes in combination with FAIMS. We demonstrate that different compensation voltages (CVs) for FAIMS are optimal for DDA and DIA, respectively. Combining DIA with FAIMS using single CVs, the instrument surpasses 2500 peptides identified per minute. This enables quantification of >5000 proteins with short online LC gradients delivered by the Evosep One LC system allowing acquisition of 60 samples per day. The raw sensitivity of the instrument is evaluated by analyzing 5 ng of a HeLa digest from which >1000 proteins were reproducibly identified with 5 min LC gradients using DIA-FAIMS. To demonstrate the versatility of the instrument, we recorded an organ-wide map of proteome expression across 12 rat tissues quantified by tandem mass tags and label-free quantification using DIA with FAIMS to a depth of >10,000 proteins.
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Affiliation(s)
- Dorte B Bekker-Jensen
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DENMARK
| | - Ana Martínez-Val
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DENMARK
| | - Sophia Steigerwald
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DENMARK
| | - Patrick Rüther
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DENMARK
| | | | | | | | | | - Jesper V Olsen
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DENMARK.
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29
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Ding F, Zhao Y, Liu H, Zhang W. Core–shell magnetic microporous covalent organic framework with functionalized Ti(iv) for selective enrichment of phosphopeptides. Analyst 2020; 145:4341-4351. [DOI: 10.1039/d0an00038h] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We fabricated a core-shell magnetic Ti4+-functionalized covalent organic framework composite to selectively capture phosphopeptides in biosamples. This method is applicable to achieve rapid, selective and efficient phosphopeptide analysis.
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Affiliation(s)
- Fengjuan Ding
- Shanghai Key Laboratory of Functional Materials Chemistry
- School of Chemistry and Molecular Engineering
- East China University of Science and Technology
- Shanghai 200237
- People’ s Republic of China
| | - Yameng Zhao
- Shanghai Key Laboratory of Functional Materials Chemistry
- School of Chemistry and Molecular Engineering
- East China University of Science and Technology
- Shanghai 200237
- People’ s Republic of China
| | - Haiyan Liu
- Shanghai Key Laboratory of Functional Materials Chemistry
- School of Chemistry and Molecular Engineering
- East China University of Science and Technology
- Shanghai 200237
- People’ s Republic of China
| | - Weibing Zhang
- Shanghai Key Laboratory of Functional Materials Chemistry
- School of Chemistry and Molecular Engineering
- East China University of Science and Technology
- Shanghai 200237
- People’ s Republic of China
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30
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Cao L, Zhao Y, Chu Z, Zhang X, Zhang W. Core-shell magnetic bimetallic MOF material for synergistic enrichment of phosphopeptides. Talanta 2020; 206:120165. [DOI: 10.1016/j.talanta.2019.120165] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 07/13/2019] [Accepted: 07/18/2019] [Indexed: 02/07/2023]
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31
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Leutert M, Rodríguez‐Mias RA, Fukuda NK, Villén J. R2-P2 rapid-robotic phosphoproteomics enables multidimensional cell signaling studies. Mol Syst Biol 2019; 15:e9021. [PMID: 31885202 PMCID: PMC6920700 DOI: 10.15252/msb.20199021] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 11/14/2019] [Accepted: 11/18/2019] [Indexed: 01/17/2023] Open
Abstract
Recent developments in proteomics have enabled signaling studies where > 10,000 phosphosites can be routinely identified and quantified. Yet, current analyses are limited in throughput, reproducibility, and robustness, hampering experiments that involve multiple perturbations, such as those needed to map kinase-substrate relationships, capture pathway crosstalks, and network inference analysis. To address these challenges, we introduce rapid-robotic phosphoproteomics (R2-P2), an end-to-end automated method that uses magnetic particles to process protein extracts to deliver mass spectrometry-ready phosphopeptides. R2-P2 is rapid, robust, versatile, and high-throughput. To showcase the method, we applied it, in combination with data-independent acquisition mass spectrometry, to study signaling dynamics in the mitogen-activated protein kinase (MAPK) pathway in yeast. Our results reveal broad and specific signaling events along the mating, the high-osmolarity glycerol, and the invasive growth branches of the MAPK pathway, with robust phosphorylation of downstream regulatory proteins and transcription factors. Our method facilitates large-scale signaling studies involving hundreds of perturbations opening the door to systems-level studies aiming to capture signaling complexity.
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Affiliation(s)
- Mario Leutert
- Department of Genome SciencesUniversity of WashingtonSeattleWAUSA
| | | | - Noelle K Fukuda
- Department of Genome SciencesUniversity of WashingtonSeattleWAUSA
| | - Judit Villén
- Department of Genome SciencesUniversity of WashingtonSeattleWAUSA
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32
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Martinez VG, Pankova V, Krasny L, Singh T, Makris S, White IJ, Benjamin AC, Dertschnig S, Horsnell HL, Kriston-Vizi J, Burden JJ, Huang PH, Tape CJ, Acton SE. Fibroblastic Reticular Cells Control Conduit Matrix Deposition during Lymph Node Expansion. Cell Rep 2019; 29:2810-2822.e5. [PMID: 31775047 PMCID: PMC6899512 DOI: 10.1016/j.celrep.2019.10.103] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 10/09/2019] [Accepted: 10/25/2019] [Indexed: 12/11/2022] Open
Abstract
Lymph nodes (LNs) act as filters, constantly sampling peripheral cues. This is facilitated by the conduit network, a tubular structure of aligned extracellular matrix (ECM) fibrils ensheathed by fibroblastic reticular cells (FRCs). LNs undergo rapid 3- to 5-fold expansion during adaptive immune responses, but these ECM-rich structures are not permanently damaged. Whether conduit flow or filtering function is affected during LN expansion is unknown. Here, we show that conduits are partially disrupted during acute LN expansion, but FRC-FRC contacts remain connected. We reveal that polarized FRCs deposit ECM basolaterally using LL5-β and that ECM production is regulated at transcriptional and secretory levels by the C-type lectin CLEC-2, expressed by dendritic cells. Inflamed LNs maintain conduit size exclusion, and flow is disrupted but persists, indicating the robustness of this structure despite rapid tissue expansion. We show how dynamic communication between peripheral tissues and LNs provides a mechanism to prevent inflammation-induced fibrosis in lymphoid tissue.
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Affiliation(s)
- Victor G Martinez
- Stromal Immunology Group, MRC Laboratory for Molecular Cell Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Valeriya Pankova
- Stromal Immunology Group, MRC Laboratory for Molecular Cell Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Lukas Krasny
- Division of Molecular Pathology, Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
| | - Tanya Singh
- Bioinformatics Image Core, MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
| | - Spyridon Makris
- Stromal Immunology Group, MRC Laboratory for Molecular Cell Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Ian J White
- Electron Microscopy Facility, MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
| | - Agnesska C Benjamin
- Stromal Immunology Group, MRC Laboratory for Molecular Cell Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Simone Dertschnig
- UCL Institute of Immunity and Transplantation, University College London, London NW3 2PF, UK
| | - Harry L Horsnell
- Stromal Immunology Group, MRC Laboratory for Molecular Cell Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Janos Kriston-Vizi
- Bioinformatics Image Core, MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
| | - Jemima J Burden
- Electron Microscopy Facility, MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
| | - Paul H Huang
- Division of Molecular Pathology, Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
| | - Christopher J Tape
- Cell Communication Lab, Department of Oncology, University College London Cancer Institute, 72 Huntley Street, London WC1E 6DD, UK
| | - Sophie E Acton
- Stromal Immunology Group, MRC Laboratory for Molecular Cell Biology, University College London, Gower Street, London WC1E 6BT, UK.
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33
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Fert-Bober J, Murray CI, Parker SJ, Van Eyk JE. Precision Profiling of the Cardiovascular Post-Translationally Modified Proteome: Where There Is a Will, There Is a Way. Circ Res 2019; 122:1221-1237. [PMID: 29700069 DOI: 10.1161/circresaha.118.310966] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
There is an exponential increase in biological complexity as initial gene transcripts are spliced, translated into amino acid sequence, and post-translationally modified. Each protein can exist as multiple chemical or sequence-specific proteoforms, and each has the potential to be a critical mediator of a physiological or pathophysiological signaling cascade. Here, we provide an overview of how different proteoforms come about in biological systems and how they are most commonly measured using mass spectrometry-based proteomics and bioinformatics. Our goal is to present this information at a level accessible to every scientist interested in mass spectrometry and its application to proteome profiling. We will specifically discuss recent data linking various protein post-translational modifications to cardiovascular disease and conclude with a discussion for enablement and democratization of proteomics across the cardiovascular and scientific community. The aim is to inform and inspire the readership to explore a larger breadth of proteoform, particularity post-translational modifications, related to their particular areas of expertise in cardiovascular physiology.
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Affiliation(s)
- Justyna Fert-Bober
- From the Advanced Clinical BioSystems Research Institute, Smidt Heart Institute, Department of Medicine, Cedars Sinai Medical Center, Los Angeles, CA
| | - Christopher I Murray
- From the Advanced Clinical BioSystems Research Institute, Smidt Heart Institute, Department of Medicine, Cedars Sinai Medical Center, Los Angeles, CA
| | - Sarah J Parker
- From the Advanced Clinical BioSystems Research Institute, Smidt Heart Institute, Department of Medicine, Cedars Sinai Medical Center, Los Angeles, CA.
| | - Jennifer E Van Eyk
- From the Advanced Clinical BioSystems Research Institute, Smidt Heart Institute, Department of Medicine, Cedars Sinai Medical Center, Los Angeles, CA
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34
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Xiao J, Yang SS, Wu JX, Wang H, Yu X, Shang W, Chen GQ, Gu ZY. Highly Selective Capture of Monophosphopeptides by Two-Dimensional Metal–Organic Framework Nanosheets. Anal Chem 2019; 91:9093-9101. [DOI: 10.1021/acs.analchem.9b01581] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Jing Xiao
- Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China
| | - Shi-Shu Yang
- Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China
| | - Jian-Xiang Wu
- Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China
| | - He Wang
- State Key Laboratory of Pharmaceutical Biotechnology, MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, 12 Xuefu Avenue, Nanjing, 210061, China
| | - Xizhong Yu
- Key Laboratory for Metabolic Diseases in Chinese Medicine, First College of Clinical Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Wenbin Shang
- Key Laboratory for Metabolic Diseases in Chinese Medicine, First College of Clinical Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Gui-Quan Chen
- State Key Laboratory of Pharmaceutical Biotechnology, MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, 12 Xuefu Avenue, Nanjing, 210061, China
| | - Zhi-Yuan Gu
- Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China
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35
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Dziomba S, Pawelec A, Ciura K, Dolegowska M, Klimowska A, Rodzaj W, Guerrouache M, Carbonnier B, Wielgomas B. Low-cost and green dispersive solid phase extraction of hydrophilic compounds using titanium dioxide nanoparticles. Microchem J 2019. [DOI: 10.1016/j.microc.2018.11.051] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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36
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Hong Y, Zhao H, Pu C, Zhan Q, Sheng Q, Lan M. Hydrophilic Phytic Acid-Coated Magnetic Graphene for Titanium(IV) Immobilization as a Novel Hydrophilic Interaction Liquid Chromatography-Immobilized Metal Affinity Chromatography Platform for Glyco- and Phosphopeptide Enrichment with Controllable Selectivity. Anal Chem 2018; 90:11008-11015. [PMID: 30136585 DOI: 10.1021/acs.analchem.8b02614] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In this work, multifunctional Ti4+-immobilized phytic acid-modified magnetic graphene (denoted as MagG@PEI@PA-Ti4+) nanocomposites were fabricated through a facile route for simultaneous/respective enrichment of N-glyco- and phosphopeptides. Phytic acid (PA), with six phosphate groups, possesses excellent hydrophilicity and metal ion coordination ability, which endowed the MagG@PEI@PA-Ti4+ with combined properties of immobilized metal ion affinity chromatography (IMAC)- and hydrophilic interaction liquid chromatography (HILIC)-based materials. On the basis of the different binding ability of N-glyco- and phosphopeptides on MagG@PEI@PA-Ti4+, the MagG@PEI@PA-Ti4+ nanocomposites could enrich N-glyco- and phosphopeptides simultaneously or respectively by using different enrichment conditions, achieving controllable selective enrichment of N-glyco- and phosphopeptides. The proposed nanocomposites demonstrated an outstanding performance for selective enrichment of N-glycopeptides (selectivity, 1:1000 molar ratios of IgG/BSA; sensitivity, 0.5 fmol/μL IgG; loading capacity, 300 mg g-1; recovery, >90%) and phosphopeptides (selectivity, 1:5000 molar ratios of α-casein/BSA; sensitivity, 0.1 fmol/μL α-casein; loading capacity, 100 mg g-1; recovery, >90%). Taking advantage of these merits, a total of 393 N-glycopeptides derived from 259 glycoproteins and 574 phosphopeptides derived from 341 phosphoproteins were identified from 200 μg of HeLa cell extracts through a single-step enrichment using MagG@PEI@PA-Ti4+.
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Affiliation(s)
- Yayun Hong
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry and Molecular Engineering , East China University of Science and Technology , Shanghai 200237 , People's Republic of China
| | - Hongli Zhao
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry and Molecular Engineering , East China University of Science and Technology , Shanghai 200237 , People's Republic of China
| | - Chenlu Pu
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry and Molecular Engineering , East China University of Science and Technology , Shanghai 200237 , People's Republic of China
| | - Qiliang Zhan
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry and Molecular Engineering , East China University of Science and Technology , Shanghai 200237 , People's Republic of China
| | - Qianying Sheng
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry and Molecular Engineering , East China University of Science and Technology , Shanghai 200237 , People's Republic of China
| | - Minbo Lan
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry and Molecular Engineering , East China University of Science and Technology , Shanghai 200237 , People's Republic of China.,State Key Laboratory of Bioreactor Engineering , East China University of Science and Technology , Shanghai 200237 , People's Republic of China
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37
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Yi L, Shi T, Gritsenko MA, X'avia Chan CY, Fillmore TL, Hess BM, Swensen AC, Liu T, Smith RD, Wiley HS, Qian WJ. Targeted Quantification of Phosphorylation Dynamics in the Context of EGFR-MAPK Pathway. Anal Chem 2018; 90:5256-5263. [PMID: 29584399 DOI: 10.1021/acs.analchem.8b00071] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Large-scale phosphoproteomics with coverage of over 10,000 sites of phosphorylation have now been routinely achieved with advanced mass spectrometry (MS)-based workflows. However, accurate targeted MS-based quantification of phosphorylation dynamics, an important direction for gaining quantitative understanding of signaling pathways or networks, has been much less investigated. Herein, we report an assessment of the targeted workflow in the context of signal transduction pathways, using the epidermal growth factor receptor (EGFR)-mitogen-activated protein kinase (MAPK) pathway as our model. A total of 43 phosphopeptides from the EGFR-MAPK pathway were selected for the study. The recovery and sensitivity of two commonly used enrichment methods, immobilized metal affinity chromatography (IMAC) and titanium oxide (TiO2), combined with selected reaction monitoring (SRM)-MS were evaluated. The recovery of phosphopeptides by IMAC and TiO2 enrichment was quantified to be 38 ± 5% and 58 ± 20%, respectively, based on internal standards. Moreover, both enrichment methods provided comparable sensitivity from 1 to 100 μg starting peptides. Robust quantification was consistently achieved for most targeted phosphopeptides when starting with 25-100 μg peptides. However, the numbers of quantified targets significantly dropped when peptide samples were in the 1-25 μg range. Finally, IMAC-SRM was applied to quantify signaling dynamics of EGFR-MAPK pathway in Hs578T cells following 10 ng/mL EGF treatment. The kinetics of phosphorylation clearly revealed early and late phases of phosphorylation, even for very low abundance proteins. These results demonstrate the feasibility of robust targeted quantification of phosphorylation dynamics for specific pathways, even starting with relatively small amounts of protein.
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38
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Ni-functionalized submicron mesoporous silica particles as a sorbent for metal affinity chromatography. J Chromatogr A 2017; 1513:140-148. [DOI: 10.1016/j.chroma.2017.07.043] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 07/11/2017] [Accepted: 07/11/2017] [Indexed: 11/24/2022]
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39
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Offenburger SL, Bensaddek D, Murillo AB, Lamond AI, Gartner A. Comparative genetic, proteomic and phosphoproteomic analysis of C. elegans embryos with a focus on ham-1/STOX and pig-1/MELK in dopaminergic neuron development. Sci Rep 2017; 7:4314. [PMID: 28659600 PMCID: PMC5489525 DOI: 10.1038/s41598-017-04375-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 05/12/2017] [Indexed: 11/09/2022] Open
Abstract
Asymmetric cell divisions are required for cellular diversity and defects can lead to altered daughter cell fates and numbers. In a genetic screen for C. elegans mutants with defects in dopaminergic head neuron specification or differentiation, we isolated a new allele of the transcription factor HAM-1 [HSN (Hermaphrodite-Specific Neurons) Abnormal Migration]. Loss of both HAM-1 and its target, the kinase PIG-1 [PAR-1(I)-like Gene], leads to abnormal dopaminergic head neuron numbers. We identified discrete genetic relationships between ham-1, pig-1 and apoptosis pathway genes in dopaminergic head neurons. We used an unbiased, quantitative mass spectrometry-based proteomics approach to characterise direct and indirect protein targets and pathways that mediate the effects of PIG-1 kinase loss in C. elegans embryos. Proteins showing changes in either abundance, or phosphorylation levels, between wild-type and pig-1 mutant embryos are predominantly connected with processes including cell cycle, asymmetric cell division, apoptosis and actomyosin-regulation. Several of these proteins play important roles in C. elegans development. Our data provide an in-depth characterisation of the C. elegans wild-type embryo proteome and phosphoproteome and can be explored via the Encyclopedia of Proteome Dynamics (EPD) - an open access, searchable online database.
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Affiliation(s)
- Sarah-Lena Offenburger
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Dalila Bensaddek
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Alejandro Brenes Murillo
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Angus I Lamond
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Anton Gartner
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK.
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Gruber W, Scheidt T, Aberger F, Huber CG. Understanding cell signaling in cancer stem cells for targeted therapy - can phosphoproteomics help to reveal the secrets? Cell Commun Signal 2017; 15:12. [PMID: 28356110 PMCID: PMC5372284 DOI: 10.1186/s12964-017-0166-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 03/13/2017] [Indexed: 12/11/2022] Open
Abstract
Background Cancer represents heterogeneous and aberrantly proliferative manifestations composed of (epi)genetically and phenotypically distinct cells with a common clonal origin. Cancer stem cells (CSC) make up a rare subpopulation with the remarkable capacity to initiate, propagate and spread a malignant disease. Furthermore, CSC show increased therapy resistance, thereby contributing to disease relapse. Elimination of CSC, therefore, is a crucial aim to design efficacious treatments for long-term survival of cancer patients. In this article, we highlight the nature of CSC and propose that phosphoproteomics based on unbiased high-performance liquid chromatography-mass spectrometry provides a powerful tool to decipher the molecular CSC programs. Detailed knowledge about the regulation of signaling processes in CSC is a prerequisite for the development of patient-tailored multi-modal treatments including the elimination of rare CSC. Main body Phosphorylation is a crucial post-translational modification regulating a plethora of both intra- and intercellular communication processes in normal and malignant cells. Small-molecule targeting of kinases has proven successful in the therapy, but the high rates of relapse and failure to stem malignant spread suggest that these kinase inhibitors largely spare CSC. Studying the kinetics of global phosphorylation patterns in an unbiased manner is, therefore, required to improve strategies and successful treatments within multi-modal therapeutic regimens by targeting the malignant behavior of CSC. The phosphoproteome comprises all phosphoproteins within a cell population that can be analyzed by phosphoproteomics, allowing the investigation of thousands of phosphorylation events. One major aspect is the perception of events underlying the activation and deactivation of kinases and phosphatases in oncogenic signaling pathways. Thus, not only can this tool be harnessed to better understand cellular processes such as those controlling CSC, but also applied to identify novel drug targets for targeted anti-CSC therapy. Conclusion State-of-the-art phosphoproteomics approaches focusing on single cell analysis have the potential to better understand oncogenic signaling in heterogeneous cell populations including rare, yet highly malignant CSC. By eliminating the influence of heterogeneity of populations, single-cell studies will reveal novel insights also into the inter- and intratumoral communication processes controlling malignant CSC and disease progression, laying the basis for improved rational combination treatments.
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Affiliation(s)
- Wolfgang Gruber
- Department of Molecular Biology, Cancer Cluster Salzburg, Paris-Lodron University of Salzburg, Hellbrunner Strasse 34, 5020, Salzburg, Austria
| | - Tamara Scheidt
- Department of Molecular Biology, Cancer Cluster Salzburg, Paris-Lodron University of Salzburg, Hellbrunner Strasse 34, 5020, Salzburg, Austria
| | - Fritz Aberger
- Department of Molecular Biology, Cancer Cluster Salzburg, Paris-Lodron University of Salzburg, Hellbrunner Strasse 34, 5020, Salzburg, Austria.
| | - Christian G Huber
- Department of Molecular Biology, Cancer Cluster Salzburg, Paris-Lodron University of Salzburg, Hellbrunner Strasse 34, 5020, Salzburg, Austria.
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Hiraga SI, Ly T, Garzón J, Hořejší Z, Ohkubo YN, Endo A, Obuse C, Boulton SJ, Lamond AI, Donaldson AD. Human RIF1 and protein phosphatase 1 stimulate DNA replication origin licensing but suppress origin activation. EMBO Rep 2017; 18:403-419. [PMID: 28077461 PMCID: PMC5331243 DOI: 10.15252/embr.201641983] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 11/08/2016] [Accepted: 12/05/2016] [Indexed: 01/13/2023] Open
Abstract
The human RIF1 protein controls DNA replication, but the molecular mechanism is largely unknown. Here, we demonstrate that human RIF1 negatively regulates DNA replication by forming a complex with protein phosphatase 1 (PP1) that limits phosphorylation-mediated activation of the MCM replicative helicase. We identify specific residues on four MCM helicase subunits that show hyperphosphorylation upon RIF1 depletion, with the regulatory N-terminal domain of MCM4 being particularly strongly affected. In addition to this role in limiting origin activation, we discover an unexpected new role for human RIF1-PP1 in mediating efficient origin licensing. Specifically, during the G1 phase of the cell cycle, RIF1-PP1 protects the origin-binding ORC1 protein from untimely phosphorylation and consequent degradation by the proteasome. Depletion of RIF1 or inhibition of PP1 destabilizes ORC1, thereby reducing origin licensing. Consistent with reduced origin licensing, RIF1-depleted cells exhibit increased spacing between active origins. Human RIF1 therefore acts as a PP1-targeting subunit that regulates DNA replication positively by stimulating the origin licensing step, and then negatively by counteracting replication origin activation.
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Affiliation(s)
- Shin-Ichiro Hiraga
- Institute of Medical Sciences, School of Medicine, Medical Sciences & Nutrition, University of Aberdeen, Aberdeen, UK
| | - Tony Ly
- Centre for Gene Regulation & Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Javier Garzón
- Institute of Medical Sciences, School of Medicine, Medical Sciences & Nutrition, University of Aberdeen, Aberdeen, UK
| | - Zuzana Hořejší
- The Francis Crick Institute, Clare Hall Laboratories, South Mimms, UK
| | - Yoshi-Nobu Ohkubo
- Graduate School of Life Science, Hokkaido University, Sapporo Hokkaido, Japan
| | - Akinori Endo
- Centre for Gene Regulation & Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Chikashi Obuse
- Graduate School of Life Science, Hokkaido University, Sapporo Hokkaido, Japan
| | - Simon J Boulton
- The Francis Crick Institute, Clare Hall Laboratories, South Mimms, UK
| | - Angus I Lamond
- Centre for Gene Regulation & Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Anne D Donaldson
- Institute of Medical Sciences, School of Medicine, Medical Sciences & Nutrition, University of Aberdeen, Aberdeen, UK
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Leitner A, Sakeye M, Zimmerli CE, Smått JH. Insights into chemoselectivity principles in metal oxide affinity chromatography using tailored nanocast metal oxide microspheres and mass spectrometry-based phosphoproteomics. Analyst 2017; 142:1993-2003. [DOI: 10.1039/c7an00570a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Custom-made nanocast metal oxide materials provide new insights into the mechanisms of metal oxide affinity chromatography, a method widely used to study proteome-wide protein phosphorylation.
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Affiliation(s)
- Alexander Leitner
- Department of Biology
- Institute of Molecular Systems Biology
- ETH Zurich
- 8093 Zurich
- Switzerland
| | - Motolani Sakeye
- Laboratory of Physical Chemistry and Center of Functional Materials
- Åbo Akademi University
- 20500 Turku
- Finland
| | | | - Jan-Henrik Smått
- Laboratory of Physical Chemistry and Center of Functional Materials
- Åbo Akademi University
- 20500 Turku
- Finland
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Tape CJ, Jørgensen C. Cell-Specific Labeling for Analyzing Bidirectional Signaling by Mass Spectrometry. Methods Mol Biol 2017; 1636:219-234. [PMID: 28730482 DOI: 10.1007/978-1-4939-7154-1_14] [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] [Indexed: 02/11/2024]
Abstract
Cell-specific proteome labeling enables global proteome-wide analysis of cell signaling in heterotypic co-cultures. Such approaches have provided unique insight in contact-initiated receptor tyrosine kinase signaling, transfer of proteomic material between heterotypic cells, and interactions between normal and oncogenic cells. Here we describe current methods for cell-specific labeling of heterotypic cells with isotopic labeled amino acids (e.g., SILAC and CTAP). We outline the advantages and disadvantages of individual approaches, describe typical experimental scenarios, and discuss where each experimental approach is optimally applied.
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Affiliation(s)
- Christopher J Tape
- The Institute of Cancer Research, London, SW3 6JB, UK
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Claus Jørgensen
- Systems Oncology, CRUK Manchester Institute, The University of Manchester, Wilmslow Road, Manchester, M20 4QL, UK.
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Wierzbicka C, Torsetnes SB, Jensen ON, Shinde S, Sellergren B. Hierarchically templated beads with tailored pore structure for phosphopeptide capture and phosphoproteomics. RSC Adv 2017. [DOI: 10.1039/c7ra00385d] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Phosphotyrosine selective beads prepared by polymer templating at two length scales results in improved capture of larger sized peptide fragments from tryptic protein digests.
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Affiliation(s)
- Celina Wierzbicka
- Department of Biomedical Sciences
- Faculty of Health and Society
- Malmö University
- SE 205 06 Malmö
- Sweden
| | - Silje B. Torsetnes
- Department of Biochemistry and Molecular Biology and VILLUM Center for Bioanalytical Sciences
- University of Southern Denmark
- DK-5230 Odense M
- Denmark
| | - Ole N. Jensen
- Department of Biochemistry and Molecular Biology and VILLUM Center for Bioanalytical Sciences
- University of Southern Denmark
- DK-5230 Odense M
- Denmark
| | - Sudhirkumar Shinde
- Department of Biomedical Sciences
- Faculty of Health and Society
- Malmö University
- SE 205 06 Malmö
- Sweden
| | - Börje Sellergren
- Department of Biomedical Sciences
- Faculty of Health and Society
- Malmö University
- SE 205 06 Malmö
- Sweden
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45
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Peng J, Zhang H, Li X, Liu S, Zhao X, Wu J, Kang X, Qin H, Pan Z, Wu R. Dual-Metal Centered Zirconium-Organic Framework: A Metal-Affinity Probe for Highly Specific Interaction with Phosphopeptides. ACS APPLIED MATERIALS & INTERFACES 2016; 8:35012-35020. [PMID: 27983800 DOI: 10.1021/acsami.6b12630] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The highly specific affinity between probes and phosphopeptides is the fundamental interaction for selective identification of phosphoproteomes that uncover the mechanisms of signal transduction, cell cycle, enzymatic regulation, and gene expression in biological systems. In this study, a metal-affinity probe possessing both interactions of metal oxide affinity chromatography (MOAC) and immobilized metal ion affinity chromatography (IMAC) was facilely prepared by immobilizing zirconium(IV) on a zirconium-organic framework of UiO-66-NH2, which holds dual-metal centers of not only the inherent Zr-O cluster but also the immobilized Zr(IV) center. This dual-metal centered zirconium-organic framework (DZMOF) demonstrates as a highly specific metal-affinity probe toward the extraction of phosphopeptides due to the metal-affinity interactions of MOAC and IMAC toward either mono-phosphorylated or multi-phosphorylated peptides. The binding energies of zirconium 3d5/2 and 3d3/2 in this DZMOF are 183.07 and 185.47 eV, respectively, which are higher than those of the intact UiO-66-NH2 (182.84 and 185.17 eV, respectively), confirming the higher metal-affinity interaction between the DZMOF and phosphopeptides. This high metal-affinity probe presents an unprecedented strong performance in anti-nonspecific interference during the capturing of phosphopeptides of β-casein with the molar ratio of β-casein vs bovine serum albumin up to ca. 1:5000. The enrichment of phosphopeptides from a human saliva sample by DZMOF further confirms the great potential of DZMOF in the extraction of low-abundance phosphopeptides for real complex biological samples.
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Affiliation(s)
- Jiaxi Peng
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian, 116023, China
- University of Chinese Academy of Sciences , Beijing, 100049, China
| | - Hongyan Zhang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian, 116023, China
- University of Chinese Academy of Sciences , Beijing, 100049, China
| | - Xin Li
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian, 116023, China
- University of Chinese Academy of Sciences , Beijing, 100049, China
| | - Shengju Liu
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian, 116023, China
- University of Chinese Academy of Sciences , Beijing, 100049, China
| | - Xingyun Zhao
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian, 116023, China
- University of Chinese Academy of Sciences , Beijing, 100049, China
| | - Jing Wu
- Wenzhou Institute of Biomaterials and Engineering, Chinese Academy of Sciences , Wenzhou, 325000, China
| | - Xiaohui Kang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian, 116023, China
| | - Hongqiang Qin
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian, 116023, China
| | - Zaifa Pan
- College of Chemical Engineering and Materials Science, Zhejiang University of Technology , Hangzhou, 310014, China
| | - Ren'an Wu
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian, 116023, China
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Brown JAL, Ni Chonghaile T, Matchett KB, Lynam-Lennon N, Kiely PA. Big Data-Led Cancer Research, Application, and Insights. Cancer Res 2016; 76:6167-6170. [PMID: 27803103 DOI: 10.1158/0008-5472.can-16-0860] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 07/31/2016] [Indexed: 11/16/2022]
Abstract
Insights distilled from integrating multiple big-data or "omic" datasets have revealed functional hierarchies of molecular networks driving tumorigenesis and modifiers of treatment response. Identifying these novel key regulatory and dysregulated elements is now informing personalized medicine. Crucially, although there are many advantages to this approach, there are several key considerations to address. Here, we examine how this big data-led approach is impacting many diverse areas of cancer research, through review of the key presentations given at the Irish Association for Cancer Research Meeting and importantly how the results may be applied to positively affect patient outcomes. Cancer Res; 76(21); 6167-70. ©2016 AACR.
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Affiliation(s)
- James A L Brown
- Discipline of Surgery, School of Medicine, The Lambe Institute for Translational Research, National University of Ireland Galway, Galway, Ireland.
| | - Triona Ni Chonghaile
- Physiology & Medical Physics Department, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Kyle B Matchett
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, United Kingdom
| | - Niamh Lynam-Lennon
- Trinity Translational Medicine Institute, Department of Surgery, Trinity College Dublin, Dublin, Ireland
| | - Patrick A Kiely
- Graduate Entry Medical School, University of Limerick, Limerick, Ireland
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47
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Highly efficient enrichment of phosphopeptides by a magnetic lanthanide metal-organic framework. Talanta 2016; 159:1-6. [DOI: 10.1016/j.talanta.2016.05.075] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Revised: 05/26/2016] [Accepted: 05/29/2016] [Indexed: 11/18/2022]
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48
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Tape CJ. Systems Biology Analysis of Heterocellular Signaling. Trends Biotechnol 2016; 34:627-637. [DOI: 10.1016/j.tibtech.2016.02.016] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 02/26/2016] [Accepted: 02/29/2016] [Indexed: 10/22/2022]
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49
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Domanova W, Krycer J, Chaudhuri R, Yang P, Vafaee F, Fazakerley D, Humphrey S, James D, Kuncic Z. Unraveling Kinase Activation Dynamics Using Kinase-Substrate Relationships from Temporal Large-Scale Phosphoproteomics Studies. PLoS One 2016; 11:e0157763. [PMID: 27336693 PMCID: PMC4918924 DOI: 10.1371/journal.pone.0157763] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 06/03/2016] [Indexed: 01/04/2023] Open
Abstract
In response to stimuli, biological processes are tightly controlled by dynamic cellular signaling mechanisms. Reversible protein phosphorylation occurs on rapid time-scales (milliseconds to seconds), making it an ideal carrier of these signals. Advances in mass spectrometry-based proteomics have led to the identification of many tens of thousands of phosphorylation sites, yet for the majority of these the kinase is unknown and the underlying network topology of signaling networks therefore remains obscured. Identifying kinase substrate relationships (KSRs) is therefore an important goal in cell signaling research. Existing consensus sequence motif based prediction algorithms do not consider the biological context of KSRs, and are therefore insensitive to many other mechanisms guiding kinase-substrate recognition in cellular contexts. Here, we use temporal information to identify biologically relevant KSRs from Large-scale In Vivo Experiments (KSR-LIVE) in a data-dependent and automated fashion. First, we used available phosphorylation databases to construct a repository of existing experimentally-predicted KSRs. For each kinase in this database, we used time-resolved phosphoproteomics data to examine how its substrates changed in phosphorylation over time. Although substrates for a particular kinase clustered together, they often exhibited a different temporal pattern to the phosphorylation of the kinase. Therefore, although phosphorylation regulates kinase activity, our findings imply that substrate phosphorylation likely serve as a better proxy for kinase activity than kinase phosphorylation. KSR-LIVE can thereby infer which kinases are regulated within a biological context. Moreover, KSR-LIVE can also be used to automatically generate positive training sets for the subsequent prediction of novel KSRs using machine learning approaches. We demonstrate that this approach can distinguish between Akt and Rps6kb1, two kinases that share the same linear consensus motif, and provide evidence suggesting IRS-1 S265 as a novel Akt site. KSR-LIVE is an open-access algorithm that allows users to dissect phosphorylation signaling within a specific biological context, with the potential to be included in the standard analysis workflow for studying temporal high-throughput signal transduction data.
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Affiliation(s)
- Westa Domanova
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
- School of Physics, The University of Sydney, Sydney, NSW 2006, Australia
| | - James Krycer
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Rima Chaudhuri
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Pengyi Yang
- National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, Durham, NC 27709, United States of America
| | - Fatemeh Vafaee
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
- School of Mathematics and Statistics, The University of Sydney, Sydney, NSW 2006, Australia
| | - Daniel Fazakerley
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Sean Humphrey
- Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Martinsried, 82152, Germany
| | - David James
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
- Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia
| | - Zdenka Kuncic
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
- School of Physics, The University of Sydney, Sydney, NSW 2006, Australia
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50
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Tape CJ, Ling S, Dimitriadi M, McMahon KM, Worboys JD, Leong HS, Norrie IC, Miller CJ, Poulogiannis G, Lauffenburger DA, Jørgensen C. Oncogenic KRAS Regulates Tumor Cell Signaling via Stromal Reciprocation. Cell 2016; 165:910-20. [PMID: 27087446 PMCID: PMC4868820 DOI: 10.1016/j.cell.2016.03.029] [Citation(s) in RCA: 210] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Revised: 02/05/2016] [Accepted: 03/17/2016] [Indexed: 12/12/2022]
Abstract
Oncogenic mutations regulate signaling within both tumor cells and adjacent stromal cells. Here, we show that oncogenic KRAS (KRAS(G12D)) also regulates tumor cell signaling via stromal cells. By combining cell-specific proteome labeling with multivariate phosphoproteomics, we analyzed heterocellular KRAS(G12D) signaling in pancreatic ductal adenocarcinoma (PDA) cells. Tumor cell KRAS(G12D) engages heterotypic fibroblasts, which subsequently instigate reciprocal signaling in the tumor cells. Reciprocal signaling employs additional kinases and doubles the number of regulated signaling nodes from cell-autonomous KRAS(G12D). Consequently, reciprocal KRAS(G12D) produces a tumor cell phosphoproteome and total proteome that is distinct from cell-autonomous KRAS(G12D) alone. Reciprocal signaling regulates tumor cell proliferation and apoptosis and increases mitochondrial capacity via an IGF1R/AXL-AKT axis. These results demonstrate that oncogene signaling should be viewed as a heterocellular process and that our existing cell-autonomous perspective underrepresents the extent of oncogene signaling in cancer. VIDEO ABSTRACT.
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Affiliation(s)
- Christopher J Tape
- The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Stephanie Ling
- The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
| | - Maria Dimitriadi
- The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
| | - Kelly M McMahon
- Cancer Research UK Manchester Institute, University of Manchester, Wilmslow Road, Manchester M20 4BX, UK
| | - Jonathan D Worboys
- The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK; Cancer Research UK Manchester Institute, University of Manchester, Wilmslow Road, Manchester M20 4BX, UK
| | - Hui Sun Leong
- Cancer Research UK Manchester Institute, University of Manchester, Wilmslow Road, Manchester M20 4BX, UK
| | - Ida C Norrie
- The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK; Cancer Research UK Manchester Institute, University of Manchester, Wilmslow Road, Manchester M20 4BX, UK
| | - Crispin J Miller
- Cancer Research UK Manchester Institute, University of Manchester, Wilmslow Road, Manchester M20 4BX, UK
| | | | - Douglas A Lauffenburger
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Claus Jørgensen
- The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK; Cancer Research UK Manchester Institute, University of Manchester, Wilmslow Road, Manchester M20 4BX, UK.
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