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Rojas-Torres M, Beltrán-Camacho L, Martínez-Val A, Sánchez-Gomar I, Eslava-Alcón S, Rosal-Vela A, Jiménez-Palomares M, Doiz-Artázcoz E, Martínez-Torija M, Moreno-Luna R, Olsen JV, Duran-Ruiz MC. Unraveling the differential mechanisms of revascularization promoted by MSCs & ECFCs from adipose tissue or umbilical cord in a murine model of critical limb-threatening ischemia. J Biomed Sci 2024; 31:71. [PMID: 39004727 DOI: 10.1186/s12929-024-01059-w] [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: 01/08/2024] [Accepted: 06/25/2024] [Indexed: 07/16/2024] Open
Abstract
BACKGROUND Critical limb-threatening ischemia (CLTI) constitutes the most severe manifestation of peripheral artery disease, usually induced by atherosclerosis. CLTI patients suffer from high risk of amputation of the lower extremities and elevated mortality rates, while they have low options for surgical revascularization due to associated comorbidities. Alternatively, cell-based therapeutic strategies represent an effective and safe approach to promote revascularization. However, the variability seen in several factors such as cell combinations or doses applied, have limited their success in clinical trials, being necessary to reach a consensus regarding the optimal "cellular-cocktail" prior further application into the clinic. To achieve so, it is essential to understand the mechanisms by which these cells exert their regenerative properties. Herein, we have evaluated, for the first time, the regenerative and vasculogenic potential of a combination of endothelial colony forming cells (ECFCs) and mesenchymal stem cells (MSCs) isolated from adipose-tissue (AT), compared with ECFCs from umbilical cord blood (CB-ECFCs) and AT-MSCs, in a murine model of CLTI. METHODS Balb-c nude mice (n:32) were distributed in four different groups (n:8/group): control shams, and ischemic mice (after femoral ligation) that received 50 µl of physiological serum alone or a cellular combination of AT-MSCs with either CB-ECFCs or AT-ECFCs. Follow-up of blood flow reperfusion and ischemic symptoms was carried out for 21 days, when mice were sacrificed to evaluate vascular density formation. Moreover, the long-term molecular changes in response to CLTI and both cell combinations were analyzed in a proteomic quantitative approach. RESULTS AT-MSCs with either AT- or CB-ECFCs, promoted a significant recovery of blood flow in CLTI mice 21 days post-ischemia. Besides, they modulated the inflammatory and necrotic related processes, although the CB group presented the slowest ischemic progression along the assay. Moreover, many proteins involved in the repairing mechanisms promoted by cell treatments were identified. CONCLUSIONS The combination of AT-MSCs with AT-ECFCs or with CB-ECFCs promoted similar revascularization in CLTI mice, by restoring blood flow levels, together with the modulation of the inflammatory and necrotic processes, and reduction of muscle damage. The protein changes identified are representative of the molecular mechanisms involved in ECFCs and MSCs-induced revascularization (immune response, vascular repair, muscle regeneration, etc.).
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Affiliation(s)
- Marta Rojas-Torres
- Biomedicine, Biotechnology and Public Health Department, University of Cadiz, Cadiz, 11002, Spain
- Biomedical Research and Innovation Institute of Cadiz (INiBICA), Cadiz, 11002, Spain
| | - Lucía Beltrán-Camacho
- Cell Biology, Physiology and Immunology Department, University of Cordoba, Cordoba, 14004, Spain
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Cordoba, 14004, Spain
| | - Ana Martínez-Val
- National Center of Cardiovascular Research Carlos III (CNIC), Madrid, 28029, Spain
| | - Ismael Sánchez-Gomar
- Biomedicine, Biotechnology and Public Health Department, University of Cadiz, Cadiz, 11002, Spain
- Biomedical Research and Innovation Institute of Cadiz (INiBICA), Cadiz, 11002, Spain
| | - Sara Eslava-Alcón
- Biomedicine, Biotechnology and Public Health Department, University of Cadiz, Cadiz, 11002, Spain
- Biomedical Research and Innovation Institute of Cadiz (INiBICA), Cadiz, 11002, Spain
| | - Antonio Rosal-Vela
- Biomedicine, Biotechnology and Public Health Department, University of Cadiz, Cadiz, 11002, Spain
- Biomedical Research and Innovation Institute of Cadiz (INiBICA), Cadiz, 11002, Spain
| | - Margarita Jiménez-Palomares
- Biomedicine, Biotechnology and Public Health Department, University of Cadiz, Cadiz, 11002, Spain
- Biomedical Research and Innovation Institute of Cadiz (INiBICA), Cadiz, 11002, Spain
| | - Esther Doiz-Artázcoz
- Angiology & Vascular Surgery Unit, Hospital Universitario Puerta del Mar, Cadiz, Spain
| | - Mario Martínez-Torija
- Pathophysiology and Regenerative Medicine Group, Hospital Nacional de Parapléjicos (SESCAM), Toledo, 45071, Spain
- Nursing department, Hospital Universitario de Toledo (SESCAM), Toledo, 45071, Spain
| | - Rafael Moreno-Luna
- Pathophysiology and Regenerative Medicine Group, Hospital Nacional de Parapléjicos (SESCAM), Toledo, 45071, Spain.
- Cooperative Research Network Orientated to Health Results, Vascular Brain Diseases, RICORS-ICTUS, SESCAM, Toledo, Spain.
| | - Jesper V Olsen
- Novo Nordisk Foundation Center for Protein Research, Copenhagen, Denmark
| | - Ma Carmen Duran-Ruiz
- Biomedicine, Biotechnology and Public Health Department, University of Cadiz, Cadiz, 11002, Spain.
- Biomedical Research and Innovation Institute of Cadiz (INiBICA), Cadiz, 11002, Spain.
- Biomedicine, Biotechnology and Public Health Department, Science Faculty, Cádiz University. Torre Sur. Avda. República Saharaui S/N, Polígono Río San Pedro, Puerto Real, Cádiz, 11519, Spain.
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Goel RK, Bithi N, Emili A. Trends in co-fractionation mass spectrometry: A new gold-standard in global protein interaction network discovery. Curr Opin Struct Biol 2024; 88:102880. [PMID: 38996623 DOI: 10.1016/j.sbi.2024.102880] [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: 04/13/2024] [Revised: 06/13/2024] [Accepted: 06/19/2024] [Indexed: 07/14/2024]
Abstract
Co-fractionation mass spectrometry (CF-MS) uses biochemical fractionation to isolate and characterize macromolecular complexes from cellular lysates without the need for affinity tagging or capture. In recent years, this has emerged as a powerful technique for elucidating global protein-protein interaction networks in a wide variety of biospecimens. This review highlights the latest advancements in CF-MS experimental workflows including machine learning-guided analyses, for uncovering dynamic and high-resolution protein interaction landscapes with enhanced sensitivity, accuracy and throughput, enabling better biophysical characterization of endogenous protein complexes. By addressing challenges and emergent opportunities in the field, this review underscores the transformative potential of CF-MS in advancing our understanding of functional protein interaction networks in health and disease.
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Affiliation(s)
- Raghuveera Kumar Goel
- Division of Oncology, Division of Oncological Sciences, Knight Cancer Institute, Oregon Health and Science University (OHSU), Portland, OR, USA.
| | - Nazmin Bithi
- Division of Oncology, Division of Oncological Sciences, Knight Cancer Institute, Oregon Health and Science University (OHSU), Portland, OR, USA
| | - Andrew Emili
- Division of Oncology, Division of Oncological Sciences, Knight Cancer Institute, Oregon Health and Science University (OHSU), Portland, OR, USA.
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3
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Edman NI, Phal A, Redler RL, Schlichthaerle T, Srivatsan SR, Ehnes DD, Etemadi A, An SJ, Favor A, Li Z, Praetorius F, Gordon M, Vincent T, Marchiano S, Blakely L, Lin C, Yang W, Coventry B, Hicks DR, Cao L, Bethel N, Heine P, Murray A, Gerben S, Carter L, Miranda M, Negahdari B, Lee S, Trapnell C, Zheng Y, Murry CE, Schweppe DK, Freedman BS, Stewart L, Ekiert DC, Schlessinger J, Shendure J, Bhabha G, Ruohola-Baker H, Baker D. Modulation of FGF pathway signaling and vascular differentiation using designed oligomeric assemblies. Cell 2024; 187:3726-3740.e43. [PMID: 38861993 PMCID: PMC11246234 DOI: 10.1016/j.cell.2024.05.025] [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: 12/16/2022] [Revised: 02/14/2024] [Accepted: 05/13/2024] [Indexed: 06/13/2024]
Abstract
Many growth factors and cytokines signal by binding to the extracellular domains of their receptors and driving association and transphosphorylation of the receptor intracellular tyrosine kinase domains, initiating downstream signaling cascades. To enable systematic exploration of how receptor valency and geometry affect signaling outcomes, we designed cyclic homo-oligomers with up to 8 subunits using repeat protein building blocks that can be modularly extended. By incorporating a de novo-designed fibroblast growth factor receptor (FGFR)-binding module into these scaffolds, we generated a series of synthetic signaling ligands that exhibit potent valency- and geometry-dependent Ca2+ release and mitogen-activated protein kinase (MAPK) pathway activation. The high specificity of the designed agonists reveals distinct roles for two FGFR splice variants in driving arterial endothelium and perivascular cell fates during early vascular development. Our designed modular assemblies should be broadly useful for unraveling the complexities of signaling in key developmental transitions and for developing future therapeutic applications.
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Affiliation(s)
- Natasha I Edman
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA 98195, USA; Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA
| | - Ashish Phal
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA; Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Rachel L Redler
- Department of Cell Biology, New York University School of Medicine, New York, NY 10016, USA
| | - Thomas Schlichthaerle
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Sanjay R Srivatsan
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Devon Duron Ehnes
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA
| | - Ali Etemadi
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Medical Biotechnology Department, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences (TUMS), Tehran, Iran
| | - Seong J An
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Andrew Favor
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Zhe Li
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Florian Praetorius
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Max Gordon
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA
| | - Thomas Vincent
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA; Department of Bioengineering, University of Washington, Seattle, WA 98195, USA; Division of Nephrology, Department of Medicine, University of Washington School of Medicine, Seattle, WA 98109, USA
| | - Silvia Marchiano
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA
| | - Leslie Blakely
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA
| | - Chuwei Lin
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Wei Yang
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Brian Coventry
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Derrick R Hicks
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Longxing Cao
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Neville Bethel
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Piper Heine
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Analisa Murray
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Stacey Gerben
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Lauren Carter
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Marcos Miranda
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Babak Negahdari
- Medical Biotechnology Department, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences (TUMS), Tehran, Iran
| | - Sangwon Lee
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Cole Trapnell
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA; Allen Discovery Center for Cell Lineage Tracing, Seattle, WA 98109, USA
| | - Ying Zheng
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA; Department of Bioengineering, University of Washington, Seattle, WA 98195, USA; Center for Cardiovascular Biology, University of Washington, Seattle WA 98109, USA
| | - Charles E Murry
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA; Department of Bioengineering, University of Washington, Seattle, WA 98195, USA; Center for Cardiovascular Biology, University of Washington, Seattle WA 98109, USA; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA; Department of Medicine/Cardiology, University of Washington, Seattle WA 98195, USA
| | - Devin K Schweppe
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Benjamin S Freedman
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA; Department of Bioengineering, University of Washington, Seattle, WA 98195, USA; Division of Nephrology, Department of Medicine, University of Washington School of Medicine, Seattle, WA 98109, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA; Kidney Research Institute, University of Washington School of Medicine, Seattle, WA 98109, USA
| | - Lance Stewart
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Damian C Ekiert
- Department of Cell Biology, New York University School of Medicine, New York, NY 10016, USA; Department of Microbiology, New York University School of Medicine, New York, NY 10016, USA
| | - Joseph Schlessinger
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA; Allen Discovery Center for Cell Lineage Tracing, Seattle, WA 98109, USA
| | - Gira Bhabha
- Department of Cell Biology, New York University School of Medicine, New York, NY 10016, USA
| | - Hannele Ruohola-Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA; Department of Bioengineering, University of Washington, Seattle, WA 98195, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
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4
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Gegner HM, Naake T, Aljakouch K, Dugourd A, Kliewer G, Müller T, Schilling D, Schneider MA, Kunze-Rohrbach N, Grünewald TGP, Hell R, Saez-Rodriguez J, Huber W, Poschet G, Krijgsveld J. A single-sample workflow for joint metabolomic and proteomic analysis of clinical specimens. Clin Proteomics 2024; 21:49. [PMID: 38969985 PMCID: PMC11225228 DOI: 10.1186/s12014-024-09501-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 06/26/2024] [Indexed: 07/07/2024] Open
Abstract
Understanding the interplay of the proteome and the metabolome helps to understand cellular regulation and response. To enable robust inferences from such multi-omics analyses, we introduced and evaluated a workflow for combined proteome and metabolome analysis starting from a single sample. Specifically, we integrated established and individually optimized protocols for metabolomic and proteomic profiling (EtOH/MTBE and autoSP3, respectively) into a unified workflow (termed MTBE-SP3), and took advantage of the fact that the protein residue of the metabolomic sample can be used as a direct input for proteome analysis. We particularly evaluated the performance of proteome analysis in MTBE-SP3, and demonstrated equivalence of proteome profiles irrespective of prior metabolite extraction. In addition, MTBE-SP3 combines the advantages of EtOH/MTBE and autoSP3 for semi-automated metabolite extraction and fully automated proteome sample preparation, respectively, thus advancing standardization and scalability for large-scale studies. We showed that MTBE-SP3 can be applied to various biological matrices (FFPE tissue, fresh-frozen tissue, plasma, serum and cells) to enable implementation in a variety of clinical settings. To demonstrate applicability, we applied MTBE-SP3 and autoSP3 to a lung adenocarcinoma cohort showing consistent proteomic alterations between tumour and non-tumour adjacent tissue independent of the method used. Integration with metabolomic data obtained from the same samples revealed mitochondrial dysfunction in tumour tissue through deregulation of OGDH, SDH family enzymes and PKM. In summary, MTBE-SP3 enables the facile and reliable parallel measurement of proteins and metabolites obtained from the same sample, benefiting from reduced sample variation and input amount. This workflow is particularly applicable for studies with limited sample availability and offers the potential to enhance the integration of metabolomic and proteomic datasets.
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Affiliation(s)
- Hagen M Gegner
- Centre for Organismal Studies (COS), Metabolomics Core Technology Platform, Heidelberg University, Im Neuenheimer Feld 360, 69120, Heidelberg, Germany
| | - Thomas Naake
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstr. 1, 69117, Heidelberg, Germany
| | - Karim Aljakouch
- Faculty of Medicine, Heidelberg University, 69120, Heidelberg, Germany
- Division Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, 69120, Heidelberg, Germany
| | - Aurelien Dugourd
- Institute for Computational Biomedicine, Bioquant, Faculty of Medicine, Heidelberg University and Heidelberg University Hospital, Im Neuenheimer Feld 130, 69120, Heidelberg, Germany
| | - Georg Kliewer
- Faculty of Medicine, Heidelberg University, 69120, Heidelberg, Germany
- Division Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, 69120, Heidelberg, Germany
| | - Torsten Müller
- Faculty of Medicine, Heidelberg University, 69120, Heidelberg, Germany
- Division Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, 69120, Heidelberg, Germany
| | - Dustin Schilling
- Institute for Computational Biomedicine, Bioquant, Faculty of Medicine, Heidelberg University and Heidelberg University Hospital, Im Neuenheimer Feld 130, 69120, Heidelberg, Germany
| | - Marc A Schneider
- Translational Research Unit, Thoraxklinik at Heidelberg University Hospital, Röntgenstraße 1, 69126, Heidelberg, Germany
- Translational Research Center Heidelberg (TLRC), Member of The German Center for Lung Research (DZL), Im Neuenheimer Feld 156, 69120, Heidelberg, Germany
| | - Nina Kunze-Rohrbach
- Centre for Organismal Studies (COS), Metabolomics Core Technology Platform, Heidelberg University, Im Neuenheimer Feld 360, 69120, Heidelberg, Germany
| | - Thomas G P Grünewald
- Division of Translational Pediatric Sarcoma Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Hopp-Children's Cancer Center (KiTZ), Heidelberg, Germany
- Institute of Pathology, Heidelberg University Hospital, Im Neuenheimer Feld 224, 69120, Heidelberg, Germany
- National Center for Tumor Diseases (NCT), NCT Heidelberg, DKFZ and Heidelberg University Hospital, Heidelberg, Germany
| | - Rüdiger Hell
- Centre for Organismal Studies (COS), Metabolomics Core Technology Platform, Heidelberg University, Im Neuenheimer Feld 360, 69120, Heidelberg, Germany
| | - Julio Saez-Rodriguez
- Institute for Computational Biomedicine, Bioquant, Faculty of Medicine, Heidelberg University and Heidelberg University Hospital, Im Neuenheimer Feld 130, 69120, Heidelberg, Germany
| | - Wolfgang Huber
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstr. 1, 69117, Heidelberg, Germany
| | - Gernot Poschet
- Centre for Organismal Studies (COS), Metabolomics Core Technology Platform, Heidelberg University, Im Neuenheimer Feld 360, 69120, Heidelberg, Germany.
| | - Jeroen Krijgsveld
- Faculty of Medicine, Heidelberg University, 69120, Heidelberg, Germany.
- Division Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, 69120, Heidelberg, Germany.
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Ciordia S, Santos FM, Dias JML, Lamas JR, Paradela A, Alvarez-Sola G, Ávila MA, Corrales F. Refinement of paramagnetic bead-based digestion protocol for automatic sample preparation using an artificial neural network. Talanta 2024; 274:125988. [PMID: 38569368 DOI: 10.1016/j.talanta.2024.125988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 03/19/2024] [Accepted: 03/22/2024] [Indexed: 04/05/2024]
Abstract
Despite technological advances in the proteomics field, sample preparation still represents the main bottleneck in mass spectrometry (MS) analysis. Bead-based protein aggregation techniques have recently emerged as an efficient, reproducible, and high-throughput alternative for protein extraction and digestion. Here, a refined paramagnetic bead-based digestion protocol is described for Opentrons® OT-2 platform (OT-2) as a versatile, reproducible, and affordable alternative for the automatic sample preparation for MS analysis. For this purpose, an artificial neural network (ANN) was applied to maximize the number of peptides without missed cleavages identified in HeLa extract by combining factors such as the quantity (μg) of trypsin/Lys-C and beads (MagReSyn® Amine), % (w/v) SDS, % (v/v) acetonitrile, and time of digestion (h). ANN model predicted the optimal conditions for the digestion of 50 μg of HeLa extract, pointing to the use of 2.5% (w/v) SDS and 300 μg of beads for sample preparation and long-term digestion (16h) with 0.15 μg Lys-C and 2.5 μg trypsin (≈1:17 ratio). Based on the results of the ANN model, the manual protocol was automated in OT-2. The performance of the automatic protocol was evaluated with different sample types, including human plasma, Arabidopsis thaliana leaves, Escherichia coli cells, and mouse tissue cortex, showing great reproducibility and low sample-to-sample variability in all cases. In addition, we tested the performance of this method in the preparation of a challenging biological fluid such as rat bile, a proximal fluid that is rich in bile salts, bilirubin, cholesterol, and fatty acids, among other MS interferents. Compared to other protocols described in the literature for the extraction and digestion of bile proteins, the method described here allowed identify 385 unique proteins, thus contributing to improving the coverage of the bile proteome.
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Affiliation(s)
- Sergio Ciordia
- Functional Proteomics Laboratory, Centro Nacional de Biotecnología, CSIC, Calle Darwin 3, Campus de Cantoblanco, 28049, Madrid, Spain
| | - Fátima Milhano Santos
- Functional Proteomics Laboratory, Centro Nacional de Biotecnología, CSIC, Calle Darwin 3, Campus de Cantoblanco, 28049, Madrid, Spain
| | - João M L Dias
- Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom; Early Cancer Institute, University of Cambridge, Cambridge, United Kingdom
| | - José Ramón Lamas
- Functional Proteomics Laboratory, Centro Nacional de Biotecnología, CSIC, Calle Darwin 3, Campus de Cantoblanco, 28049, Madrid, Spain
| | - Alberto Paradela
- Functional Proteomics Laboratory, Centro Nacional de Biotecnología, CSIC, Calle Darwin 3, Campus de Cantoblanco, 28049, Madrid, Spain
| | - Gloria Alvarez-Sola
- Hepatology Laboratory, Solid Tumors Program, Center for Applied Medical Research (CIMA), University of Navarra, 31008, Pamplona, Spain; National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Carlos III Health Institute), 28029, Madrid, Spain; IdiSNA, Navarra Institute for Health Research, 31008, Pamplona, Spain
| | - Matías A Ávila
- Hepatology Laboratory, Solid Tumors Program, Center for Applied Medical Research (CIMA), University of Navarra, 31008, Pamplona, Spain; National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Carlos III Health Institute), 28029, Madrid, Spain; IdiSNA, Navarra Institute for Health Research, 31008, Pamplona, Spain
| | - Fernando Corrales
- Functional Proteomics Laboratory, Centro Nacional de Biotecnología, CSIC, Calle Darwin 3, Campus de Cantoblanco, 28049, Madrid, Spain.
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Mehta D, Scandola S, Kennedy C, Lummer C, Gallo MCR, Grubb LE, Tan M, Scarpella E, Uhrig RG. Twilight length alters growth and flowering time in Arabidopsis via LHY/ CCA1. SCIENCE ADVANCES 2024; 10:eadl3199. [PMID: 38941453 PMCID: PMC11212724 DOI: 10.1126/sciadv.adl3199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 05/28/2024] [Indexed: 06/30/2024]
Abstract
Decades of research have uncovered how plants respond to two environmental variables that change across latitudes and over seasons: photoperiod and temperature. However, a third such variable, twilight length, has so far gone unstudied. Here, using controlled growth setups, we show that the duration of twilight affects growth and flowering time via the LHY/CCA1 clock genes in the model plant Arabidopsis. Using a series of progressively truncated no-twilight photoperiods, we also found that plants are more sensitive to twilight length compared to equivalent changes in solely photoperiods. Transcriptome and proteome analyses showed that twilight length affects reactive oxygen species metabolism, photosynthesis, and carbon metabolism. Genetic analyses suggested a twilight sensing pathway from the photoreceptors PHY E, PHY B, PHY D, and CRY2 through LHY/CCA1 to flowering modulation through the GI-FT pathway. Overall, our findings call for more nuanced models of day-length perception in plants and posit that twilight is an important determinant of plant growth and development.
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Affiliation(s)
- Devang Mehta
- Department of Biosystems, KU Leuven, B-3001 Leuven, Belgium
- Leuven Plant Institute, KU Leuven, B-3001 Leuven, Belgium
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Sabine Scandola
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Curtis Kennedy
- Department of Computing Science, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Christina Lummer
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | | | - Lauren E. Grubb
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Maryalle Tan
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Enrico Scarpella
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - R. Glen Uhrig
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2E9, Canada
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7
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Oliinyk D, Will A, Schneidmadel FR, Böhme M, Rinke J, Hochhaus A, Ernst T, Hahn N, Geis C, Lubeck M, Raether O, Humphrey SJ, Meier F. µPhos: a scalable and sensitive platform for high-dimensional phosphoproteomics. Mol Syst Biol 2024:10.1038/s44320-024-00050-9. [PMID: 38907068 DOI: 10.1038/s44320-024-00050-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 06/06/2024] [Accepted: 06/11/2024] [Indexed: 06/23/2024] Open
Abstract
Mass spectrometry has revolutionized cell signaling research by vastly simplifying the analysis of many thousands of phosphorylation sites in the human proteome. Defining the cellular response to perturbations is crucial for further illuminating the functionality of the phosphoproteome. Here we describe µPhos ('microPhos'), an accessible phosphoproteomics platform that permits phosphopeptide enrichment from 96-well cell culture and small tissue amounts in <8 h total processing time. By greatly minimizing transfer steps and liquid volumes, we demonstrate increased sensitivity, >90% selectivity, and excellent quantitative reproducibility. Employing highly sensitive trapped ion mobility mass spectrometry, we quantify ~17,000 Class I phosphosites in a human cancer cell line using 20 µg starting material, and confidently localize ~6200 phosphosites from 1 µg. This depth covers key signaling pathways, rendering sample-limited applications and perturbation experiments with hundreds of samples viable. We employ µPhos to study drug- and time-dependent response signatures in a leukemia cell line, and by quantifying 30,000 Class I phosphosites in the mouse brain we reveal distinct spatial kinase activities in subregions of the hippocampal formation.
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Affiliation(s)
- Denys Oliinyk
- Functional Proteomics, Jena University Hospital, 07747, Jena, Germany
- Comprehensive Cancer Center Central Germany, 07747, Jena, Germany
| | - Andreas Will
- Functional Proteomics, Jena University Hospital, 07747, Jena, Germany
- Comprehensive Cancer Center Central Germany, 07747, Jena, Germany
| | - Felix R Schneidmadel
- Functional Proteomics, Jena University Hospital, 07747, Jena, Germany
- Comprehensive Cancer Center Central Germany, 07747, Jena, Germany
| | - Maximilian Böhme
- Comprehensive Cancer Center Central Germany, 07747, Jena, Germany
- Klinik für Innere Medizin II, Jena University Hospital, 07747, Jena, Germany
| | - Jenny Rinke
- Comprehensive Cancer Center Central Germany, 07747, Jena, Germany
- Klinik für Innere Medizin II, Jena University Hospital, 07747, Jena, Germany
| | - Andreas Hochhaus
- Comprehensive Cancer Center Central Germany, 07747, Jena, Germany
- Klinik für Innere Medizin II, Jena University Hospital, 07747, Jena, Germany
| | - Thomas Ernst
- Comprehensive Cancer Center Central Germany, 07747, Jena, Germany
- Klinik für Innere Medizin II, Jena University Hospital, 07747, Jena, Germany
| | - Nina Hahn
- Section of Translational Neuroimmunology, Department of Neurology, Jena University Hospital, 07747, Jena, Germany
- Center for Sepsis Control and Care, Jena University Hospital, 07747, Jena, Germany
| | - Christian Geis
- Section of Translational Neuroimmunology, Department of Neurology, Jena University Hospital, 07747, Jena, Germany
- Center for Sepsis Control and Care, Jena University Hospital, 07747, Jena, Germany
| | - Markus Lubeck
- Bruker Daltonics GmbH & Co. KG, 28359, Bremen, Germany
| | | | - Sean J Humphrey
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, 3052, Victoria, Australia.
| | - Florian Meier
- Functional Proteomics, Jena University Hospital, 07747, Jena, Germany.
- Comprehensive Cancer Center Central Germany, 07747, Jena, Germany.
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8
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Yalçin Z, Lam SY, Peuscher MH, van der Torre J, Zhu S, Iyengar PV, Salas-Lloret D, de Krijger I, Moatti N, van der Lugt R, Falcone M, Cerutti A, Bleijerveld OB, Hoekman L, González-Prieto R, Jacobs JJL. UBE2D3 facilitates NHEJ by orchestrating ATM signalling through multi-level control of RNF168. Nat Commun 2024; 15:5032. [PMID: 38866770 PMCID: PMC11169547 DOI: 10.1038/s41467-024-49431-6] [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: 04/05/2024] [Accepted: 06/03/2024] [Indexed: 06/14/2024] Open
Abstract
Maintenance of genome integrity requires tight control of DNA damage response (DDR) signalling and repair, with phosphorylation and ubiquitination representing key elements. How these events are coordinated to achieve productive DNA repair remains elusive. Here we identify the ubiquitin-conjugating enzyme UBE2D3 as a regulator of ATM kinase-induced DDR that promotes non-homologous end-joining (NHEJ) at telomeres. UBE2D3 contributes to DDR-induced chromatin ubiquitination and recruitment of the NHEJ-promoting factor 53BP1, both mediated by RNF168 upon ATM activation. Additionally, UBE2D3 promotes NHEJ by limiting RNF168 accumulation and facilitating ATM-mediated phosphorylation of KAP1-S824. Mechanistically, defective KAP1-S824 phosphorylation and telomeric NHEJ upon UBE2D3-deficiency are linked to RNF168 hyperaccumulation and aberrant PP2A phosphatase activity. Together, our results identify UBE2D3 as a multi-level regulator of NHEJ that orchestrates ATM and RNF168 activities. Moreover, they reveal a negative regulatory circuit in the DDR that is constrained by UBE2D3 and consists of RNF168- and phosphatase-mediated restriction of KAP1 phosphorylation.
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Affiliation(s)
- Zeliha Yalçin
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands
| | - Shiu Yeung Lam
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands
| | - Marieke H Peuscher
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands
| | - Jaco van der Torre
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands
| | - Sha Zhu
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands
| | - Prasanna V Iyengar
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands
| | - Daniel Salas-Lloret
- Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, the Netherlands
| | - Inge de Krijger
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands
| | - Nathalie Moatti
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands
| | - Ruben van der Lugt
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands
| | - Mattia Falcone
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands
| | - Aurora Cerutti
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands
| | - Onno B Bleijerveld
- Proteomics Facility, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands
| | - Liesbeth Hoekman
- Proteomics Facility, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands
| | - Román González-Prieto
- Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, the Netherlands
- Andalusian Center for Molecular Biology and regenerative Medicine (CABIMER), Universidad de Sevilla-CSIC-Universidad-Pablo de Olavide, Sevilla, Spain
- Departamento de Biología Celular, Facultad de Biología, Universidad de Sevilla, Sevilla, Spain
| | - Jacqueline J L Jacobs
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands.
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9
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Pierre-Ferrer S, Collins B, Lukacsovich D, Wen S, Cai Y, Winterer J, Yan J, Pedersen L, Földy C, Brown SA. A phosphate transporter in VIPergic neurons of the suprachiasmatic nucleus gates locomotor activity during the light/dark transition in mice. Cell Rep 2024; 43:114220. [PMID: 38735047 DOI: 10.1016/j.celrep.2024.114220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 02/23/2024] [Accepted: 04/25/2024] [Indexed: 05/14/2024] Open
Abstract
The suprachiasmatic nucleus (SCN) encodes time of day through changes in daily firing; however, the molecular mechanisms by which the SCN times behavior are not fully understood. To identify factors that could encode day/night differences in activity, we combine patch-clamp recordings and single-cell sequencing of individual SCN neurons in mice. We identify PiT2, a phosphate transporter, as being upregulated in a population of Vip+Nms+ SCN neurons at night. Although nocturnal and typically showing a peak of activity at lights off, mice lacking PiT2 (PiT2-/-) do not reach the activity level seen in wild-type mice during the light/dark transition. PiT2 loss leads to increased SCN neuronal firing and broad changes in SCN protein phosphorylation. PiT2-/- mice display a deficit in seasonal entrainment when moving from a simulated short summer to longer winter nights. This suggests that PiT2 is responsible for timing activity and is a driver of SCN plasticity allowing seasonal entrainment.
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Affiliation(s)
- Sara Pierre-Ferrer
- Chronobiology and Sleep Research Group, Institute of Pharmacology and Toxicology, Faculties of Medicine and Science, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland.
| | - Ben Collins
- Chronobiology and Sleep Research Group, Institute of Pharmacology and Toxicology, Faculties of Medicine and Science, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland; Department of Biology, Sacred Heart University, 5151 Park Ave., Fairfield, CT 06825, USA
| | - David Lukacsovich
- Laboratory of Neural Connectivity, Brain Research Institute, Faculties of Medicine and Science, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Shao'Ang Wen
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yuchen Cai
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jochen Winterer
- Laboratory of Neural Connectivity, Brain Research Institute, Faculties of Medicine and Science, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Jun Yan
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Lene Pedersen
- Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, 8000 Aarhus, Denmark
| | - Csaba Földy
- Laboratory of Neural Connectivity, Brain Research Institute, Faculties of Medicine and Science, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland.
| | - Steven A Brown
- Chronobiology and Sleep Research Group, Institute of Pharmacology and Toxicology, Faculties of Medicine and Science, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
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10
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Lin C, Sniezek C, Giglio RM, Karki R, McGann C, Garcia BA, McFaline-Figeroa JL, Schweppe DK. Lineage-specific proteome remodeling of diverse lung cancer cells by targeted epigenetic inhibitors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.23.592075. [PMID: 38853901 PMCID: PMC11160595 DOI: 10.1101/2024.05.23.592075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Epigenetic inhibitors exhibit powerful antiproliferative and anticancer activities. However, cellular responses to small-molecule epigenetic inhibition are heterogenous and dependent on factors such as the genetic background, metabolic state, and on-/off-target engagement of individual small-molecule drugs. To determine the mechanisms that drive these heterogeneous cellular responses, we quantified chromatin, proteome, and transcriptome remodeling due to histone deacetylase inhibitor (HDACi) -treated cells derived from diverse genetic backgrounds. We utilized high-throughput sample multiplexed proteomics and integrated intelligent data acquisition methods to map proteomes of cancer cell lines in response to HDACi. We determined cell type-specific and ubiquitous cellular responses based on the quantification of 10,621 total proteins. We then established how coordinated remodeling of the proteome, transcriptome and chromatin state of HDACi treated cancer cells revealed convergent (JUN, MAP2K3, CDKN1A) and divergent (CCND3, ASF1B, BRD7) molecular phenotypes. HDACi-regulated proteins differ greatly across cell lines owing to heterogeneous molecular states of these cell lines. Finally, we demonstrated that HDACi treatment drove a highly cell-type specific response that may in part be explained by cell line-specific off-target drug engagement.
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Affiliation(s)
- Chuwei Lin
- University of Washington, Seattle, WA 98105, USA
| | | | | | - Rashmi Karki
- Washington University School of Medicine, St. Louis, MO 63110, USA
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11
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Reder A, Hentschker C, Steil L, Gesell Salazar M, Hammer E, Dhople VM, Sura T, Lissner U, Wolfgramm H, Dittmar D, Harms M, Surmann K, Völker U, Michalik S. MassSpecPreppy-An end-to-end solution for automated protein concentration determination and flexible sample digestion for proteomics applications. Proteomics 2024; 24:e2300294. [PMID: 37772677 DOI: 10.1002/pmic.202300294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/13/2023] [Accepted: 09/14/2023] [Indexed: 09/30/2023]
Abstract
In proteomics, fast, efficient, and highly reproducible sample preparation is of utmost importance, particularly in view of fast scanning mass spectrometers enabling analyses of large sample series. To address this need, we have developed the web application MassSpecPreppy that operates on the open science OT-2 liquid handling robot from Opentrons. This platform can prepare up to 96 samples at once, performing tasks like BCA protein concentration determination, sample digestion with normalization, reduction/alkylation and peptide elution into vials or loading specified peptide amounts onto Evotips in an automated and flexible manner. The performance of the developed workflows using MassSpecPreppy was compared with standard manual sample preparation workflows. The BCA assay experiments revealed an average recovery of 101.3% (SD: ± 7.82%) for the MassSpecPreppy workflow, while the manual workflow had a recovery of 96.3% (SD: ± 9.73%). The species mix used in the evaluation experiments showed that 94.5% of protein groups for OT-2 digestion and 95% for manual digestion passed the significance thresholds with comparable peptide level coefficient of variations. These results demonstrate that MassSpecPreppy is a versatile and scalable platform for automated sample preparation, producing injection-ready samples for proteomics research.
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Affiliation(s)
- Alexander Reder
- Interfaculty Institute of Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Christian Hentschker
- Interfaculty Institute of Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Leif Steil
- Interfaculty Institute of Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Manuela Gesell Salazar
- Interfaculty Institute of Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Elke Hammer
- Interfaculty Institute of Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Vishnu M Dhople
- Interfaculty Institute of Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Thomas Sura
- Interfaculty Institute of Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Ulrike Lissner
- Interfaculty Institute of Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Hannes Wolfgramm
- Interfaculty Institute of Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Denise Dittmar
- Interfaculty Institute of Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Marco Harms
- Interfaculty Institute of Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Kristin Surmann
- Interfaculty Institute of Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Uwe Völker
- Interfaculty Institute of Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Stephan Michalik
- Interfaculty Institute of Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
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12
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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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13
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Reiter MA, Bradley T, Büchel LA, Keller P, Hegedis E, Gassler T, Vorholt JA. A synthetic methylotrophic Escherichia coli as a chassis for bioproduction from methanol. Nat Catal 2024; 7:560-573. [PMID: 38828428 PMCID: PMC11136667 DOI: 10.1038/s41929-024-01137-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 02/29/2024] [Indexed: 06/05/2024]
Abstract
Methanol synthesized from captured greenhouse gases is an emerging renewable feedstock with great potential for bioproduction. Recent research has raised the prospect of methanol bioconversion to value-added products using synthetic methylotrophic Escherichia coli, as its metabolism can be rewired to enable growth solely on the reduced one-carbon compound. Here we describe the generation of an E. coli strain that grows on methanol at a doubling time of 4.3 h-comparable to many natural methylotrophs. To establish bioproduction from methanol using this synthetic chassis, we demonstrate biosynthesis from four metabolic nodes from which numerous bioproducts can be derived: lactic acid from pyruvate, polyhydroxybutyrate from acetyl coenzyme A, itaconic acid from the tricarboxylic acid cycle and p-aminobenzoic acid from the chorismate pathway. In a step towards carbon-negative chemicals and valorizing greenhouse gases, our work brings synthetic methylotrophy in E. coli within reach of industrial applications.
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Affiliation(s)
- Michael A. Reiter
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Timothy Bradley
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Lars A. Büchel
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Philipp Keller
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Emese Hegedis
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Thomas Gassler
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Julia A. Vorholt
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
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14
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Warner H, Franciosa G, van der Borg G, Coenen B, Faas F, Koenig C, de Boer R, Classens R, Maassen S, Baranov MV, Mahajan S, Dabral D, Bianchi F, van Hilten N, Risselada HJ, Roos WH, Olsen JV, Cano LQ, van den Bogaart G. Atypical cofilin signaling drives dendritic cell migration through the extracellular matrix via nuclear deformation. Cell Rep 2024; 43:113866. [PMID: 38416638 DOI: 10.1016/j.celrep.2024.113866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 10/13/2023] [Accepted: 02/08/2024] [Indexed: 03/01/2024] Open
Abstract
To mount an adaptive immune response, dendritic cells must migrate to lymph nodes to present antigens to T cells. Critical to 3D migration is the nucleus, which is the size-limiting barrier for migration through the extracellular matrix. Here, we show that inflammatory activation of dendritic cells leads to the nucleus becoming spherically deformed and enables dendritic cells to overcome the typical 2- to 3-μm diameter limit for 3D migration through gaps in the extracellular matrix. We show that the nuclear shape change is partially attained through reduced cell adhesion, whereas improved 3D migration is achieved through reprogramming of the actin cytoskeleton. Specifically, our data point to a model whereby the phosphorylation of cofilin-1 at serine 41 drives the assembly of a cofilin-actomyosin ring proximal to the nucleus and enhances migration through 3D collagen gels. In summary, these data describe signaling events through which dendritic cells deform their nucleus and enhance their migratory capacity.
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Affiliation(s)
- Harry Warner
- Department of Molecular Immunology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Giulia Franciosa
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Guus van der Borg
- Molecular Biophysics, Zernike Institute for Advanced Materials, University of Groningen, Groningen, the Netherlands
| | - Britt Coenen
- Department of Molecular Immunology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Felix Faas
- Department of Molecular Immunology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Claire Koenig
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Rinse de Boer
- Department of Molecular Immunology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - René Classens
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Sjors Maassen
- Department of Molecular Immunology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Maksim V Baranov
- Department of Molecular Immunology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Shweta Mahajan
- Department of Molecular Immunology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Deepti Dabral
- Department of Molecular Immunology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Frans Bianchi
- Department of Molecular Immunology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Niek van Hilten
- Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Herre Jelger Risselada
- Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands; Department of Physics, TU Dortmund, Dortmund, Germany
| | - Wouter H Roos
- Molecular Biophysics, Zernike Institute for Advanced Materials, University of Groningen, Groningen, the Netherlands
| | - Jesper Velgaard Olsen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Laia Querol Cano
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Geert van den Bogaart
- Department of Molecular Immunology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands; Department of Pathology and Medical Biology, University Medical Center Groningen, Groningen, the Netherlands.
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15
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Yue L, Gong T, Jiang W, Qian L, Gong W, Sun Y, Cai X, Xu H, Liu F, Wang H, Li S, Zhu Y, Zheng Z, Wu Q, Guo T. Proteomic profiling of ovarian clear cell carcinomas identifies prognostic biomarkers for chemotherapy. Proteomics 2024; 24:e2300242. [PMID: 38171885 DOI: 10.1002/pmic.202300242] [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: 06/08/2023] [Revised: 11/17/2023] [Accepted: 11/20/2023] [Indexed: 01/05/2024]
Abstract
Clear cell ovarian carcinoma (CCOC) is a relatively rare subtype of ovarian cancer (OC) with high degree of resistance to standard chemotherapy. Little is known about the underlying molecular mechanisms, and it remains a challenge to predict its prognosis after chemotherapy. Here, we first analyzed the proteome of 35 formalin-fixed paraffin-embedded (FFPE) CCOC tissue specimens from a cohort of 32 patients with CCOC (H1 cohort) and characterized 8697 proteins using data-independent acquisition mass spectrometry (DIA-MS). We then performed proteomic analysis of 28 fresh frozen (FF) CCOC tissue specimens from an independent cohort of 24 patients with CCOC (H2 cohort), leading to the identification of 9409 proteins with DIA-MS. After bioinformatics analysis, we narrowed our focus to 15 proteins significantly correlated with the recurrence free survival (RFS) in both cohorts. These proteins are mainly involved in DNA damage response, extracellular matrix (ECM), and mitochondrial metabolism. Parallel reaction monitoring (PRM)-MS was adopted to validate the prognostic potential of the 15 proteins in the H1 cohort and an independent confirmation cohort (H3 cohort). Interferon-inducible transmembrane protein 1 (IFITM1) was observed as a robust prognostic marker for CCOC in both PRM data and immunohistochemistry (IHC) data. Taken together, this study presents a CCOC proteomic data resource and a single promising protein, IFITM1, which could potentially predict the recurrence and survival of CCOC.
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Affiliation(s)
- Liang Yue
- School of Life Sciences, Fudan University, Shanghai, China
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China
- Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China
| | - Tingting Gong
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University
| | - Wenhao Jiang
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China
- Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China
| | - Liujia Qian
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China
- Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China
| | - Wangang Gong
- Zhejiang Cancer Hospital, Hangzhou, Zhejiang, China
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Yaoting Sun
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China
- Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China
| | - Xue Cai
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China
- Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China
| | - Heli Xu
- Department of Clinical Epidemiology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Fanghua Liu
- Department of Clinical Epidemiology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - He Wang
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China
- Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China
| | - Sainan Li
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China
- Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
- National Health Commission Key Laboratory of Reproductive Health, Institute of Reproductive and Child Health, Peking University, Beijing, China
| | - Yi Zhu
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China
- Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China
| | - Zhiguo Zheng
- Zhejiang Cancer Hospital, Hangzhou, Zhejiang, China
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Qijun Wu
- Department of Clinical Epidemiology, Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Tiannan Guo
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China
- Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China
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16
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Choudhury FK, Premkumar V, Zecha J, Boyd J, Gaynor AS, Guo Z, Martin T, Cimbro R, Allman EL, Hess S. Multiomics Characterization of a Less Invasive Microfluidic-Based Cell Sorting Technique. J Proteome Res 2024. [PMID: 38417049 DOI: 10.1021/acs.jproteome.3c00773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2024]
Abstract
Fluorescence-activated cell sorting (FACS) is a specialized technique to isolate specific cell subpopulations with a high level of recovery and accuracy. However, the cell sorting procedure can impact the viability and metabolic state of cells. Here, we performed a comparative study and evaluated the impact of traditional high-pressure charged droplet-based and microfluidic chip-based sorting on the metabolic and phosphoproteomic profile of different cell types. While microfluidic chip-based sorted cells more closely resembled the unsorted control group for most cell types tested, the droplet-based sorted cells showed significant metabolic and phosphoproteomic alterations. In particular, greater changes in redox and energy status were present in cells sorted with the droplet-based cell sorter along with larger shifts in proteostasis. 13C-isotope tracing analysis on cells recovering postsorting revealed that the sorter-induced suppression of mitochondrial TCA cycle activity recovered faster in the microfluidic chip-based sorted group. Apart from this, amino acid and lipid biosynthesis pathways were suppressed in sorted cells, with minimum impact and faster recovery in the microfluidic chip-based sorted group. These results indicate microfluidic chip-based sorting has a minimum impact on metabolism and is less disruptive compared to droplet-based sorting.
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Affiliation(s)
- Feroza K Choudhury
- Dynamic Omics, Centre for Genomics Research (CGR), Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, Maryland 20878, United States
| | - Viji Premkumar
- Dynamic Omics, Centre for Genomics Research (CGR), Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, Maryland 20878, United States
| | - Jana Zecha
- Dynamic Omics, Centre for Genomics Research (CGR), Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, Maryland 20878, United States
| | - Jonathan Boyd
- Dynamic Omics, Centre for Genomics Research (CGR), Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, Maryland 20878, United States
| | - Andrew S Gaynor
- Oncology Cell Therapy, ICC, Oncology R&D, AstraZeneca, Gaithersburg, Maryland 20878, United States
| | - Zengli Guo
- Biologics Engineering, Cell Therapeutics and Viral Technologies, AstraZeneca, Gaithersburg, Maryland 20878, United States
| | - Tom Martin
- Biologics Engineering, Oncology TTD, ADC, AstraZeneca, Gaithersburg, Maryland 20878, United States
| | - Raffaello Cimbro
- Dynamic Omics, Centre for Genomics Research (CGR), Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB2 0AA, United Kingdom
| | - Erik L Allman
- Dynamic Omics, Centre for Genomics Research (CGR), Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, Maryland 20878, United States
| | - Sonja Hess
- Dynamic Omics, Centre for Genomics Research (CGR), Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, Maryland 20878, United States
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17
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Dieters-Castator DZ, Manzanillo P, Yang HY, Modak RV, Rardin MJ, Gibson BW. Magnetic Bead-Based Workflow for Sensitive and Streamlined Cell Surface Proteomics. J Proteome Res 2024; 23:618-632. [PMID: 38226771 DOI: 10.1021/acs.jproteome.3c00432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2024]
Abstract
Cell surface proteins represent an important class of molecules for therapeutic targeting and cellular phenotyping. However, their enrichment and detection via mass spectrometry-based proteomics remains challenging due to low abundance, post-translational modifications, hydrophobic regions, and processing requirements. To improve their identification, we optimized a Cell-Surface Capture (CSC) workflow that incorporates magnetic bead-based processing. Using this approach, we evaluated labeling conditions (biotin tags and catalysts), enrichment specificity (streptavidin beads), missed cleavages (lysis buffers), nonenzymatic deamidation (digestion and deglycosylation buffers), and data acquisition methods (DDA, DIA, and TMT). Our findings support the use of alkoxyamine-PEG4-biotin plus 5-methoxy-anthranilic acid, SDS/urea-based lysis buffers, single-pot solid-phased-enhanced sample-preparation (SP3), and streptavidin magnetic beads for maximal surfaceome coverage. Notably, with semiautomated processing, sample handling was simplified and between ∼600 and 900 cell surface N-glycoproteins were identified from only 25-200 μg of HeLa protein. CSC also revealed significant differences between in vitro monolayer cultures and in vivo tumor xenografts of murine CT26 colon adenocarcinoma samples that may aid in target identification for drug development. Overall, the improved efficiency of the magnetic-based CSC workflow identified both previously reported and novel N-glycosites with less material and high reproducibility that should help advance the field of surfaceomics by providing insight in cellular phenotypes not previously documented.
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Affiliation(s)
| | - Paolo Manzanillo
- Inflammation, Amgen Research, South San Francisco, California 94080, United States
| | - Han-Yin Yang
- Discovery Proteomics, Amgen Research, South San Francisco, California 94080, United States
| | - Rucha V Modak
- Inflammation, Amgen Research, South San Francisco, California 94080, United States
| | - Matthew J Rardin
- Discovery Proteomics, Amgen Research, South San Francisco, California 94080, United States
| | - Bradford W Gibson
- Discovery Proteomics, Amgen Research, South San Francisco, California 94080, United States
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18
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Leutert M, Barente AS, Fukuda NK, Rodriguez-Mias RA, Villén J. The regulatory landscape of the yeast phosphoproteome. Nat Struct Mol Biol 2023; 30:1761-1773. [PMID: 37845410 PMCID: PMC10841839 DOI: 10.1038/s41594-023-01115-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 09/05/2023] [Indexed: 10/18/2023]
Abstract
The cellular ability to react to environmental fluctuations depends on signaling networks that are controlled by the dynamic activities of kinases and phosphatases. Here, to gain insight into these stress-responsive phosphorylation networks, we generated a quantitative mass spectrometry-based atlas of early phosphoproteomic responses in Saccharomyces cerevisiae exposed to 101 environmental and chemical perturbations. We report phosphosites on 59% of the yeast proteome, with 18% of the proteome harboring a phosphosite that is regulated within 5 min of stress exposure. We identify shared and perturbation-specific stress response programs, uncover loss of phosphorylation as an integral early event, and dissect the interconnected regulatory landscape of kinase-substrate networks, as we exemplify with target of rapamycin signaling. We further reveal functional organization principles of the stress-responsive phosphoproteome based on phosphorylation site motifs, kinase activities, subcellular localizations, shared functions and pathway intersections. This information-rich map of 25,000 regulated phosphosites advances our understanding of signaling networks.
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Affiliation(s)
- Mario Leutert
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
| | - Anthony S Barente
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Noelle K Fukuda
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | | | - Judit Villén
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
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19
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Rodriguez Gallo MC, Li Q, Talasila M, Uhrig RG. Quantitative Time-Course Analysis of Osmotic and Salt Stress in Arabidopsis thaliana Using Short Gradient Multi-CV FAIMSpro BoxCar DIA. Mol Cell Proteomics 2023; 22:100638. [PMID: 37704098 PMCID: PMC10663867 DOI: 10.1016/j.mcpro.2023.100638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 08/22/2023] [Accepted: 08/27/2023] [Indexed: 09/15/2023] Open
Abstract
A major limitation when undertaking quantitative proteomic time-course experimentation is the tradeoff between depth-of-analysis and speed-of-analysis. In high complexity and high dynamic range sample types, such as plant extracts, balance between resolution and time is especially apparent. To address this, we evaluate multiple compensation voltage (CV) high field asymmetric waveform ion mobility spectrometry (FAIMSpro) settings using the latest label-free single-shot Orbitrap-based DIA acquisition workflows for their ability to deeply quantify the Arabidopsis thaliana seedling proteome. Using a BoxCarDIA acquisition workflow with a -30 -50 -70 CV FAIMSpro setting, we were able to consistently quantify >5000 Arabidopsis seedling proteins over a 21-min gradient, facilitating the analysis of ∼42 samples per day. Utilizing this acquisition approach, we then quantified proteome-level changes occurring in Arabidopsis seedling shoots and roots over 24 h of salt and osmotic stress, to identify early and late stress response proteins and reveal stress response overlaps. Here, we successfully quantify >6400 shoot and >8500 root protein groups, respectively, quantifying nearly ∼9700 unique protein groups in total across the study. Collectively, we pioneer a short gradient, multi-CV FAIMSpro BoxCarDIA acquisition workflow that represents an exciting new analysis approach for undertaking quantitative proteomic time-course experimentation in plants.
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Affiliation(s)
- M C Rodriguez Gallo
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Q Li
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - M Talasila
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - R G Uhrig
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada; Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada.
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20
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Bradley D, Hogrebe A, Dandage R, Dubé AK, Leutert M, Dionne U, Chang A, Villén J, Landry CR. The fitness cost of spurious phosphorylation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.08.561337. [PMID: 37873463 PMCID: PMC10592693 DOI: 10.1101/2023.10.08.561337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
The fidelity of signal transduction requires the binding of regulatory molecules to their cognate targets. However, the crowded cell interior risks off-target interactions between proteins that are functionally unrelated. How such off-target interactions impact fitness is not generally known, but quantifying this is required to understand the constraints faced by cell systems as they evolve. Here, we use the model organism S. cerevisiae to inducibly express tyrosine kinases. Because yeast lacks bona fide tyrosine kinases, most of the resulting tyrosine phosphorylation is spurious. This provides a suitable system to measure the impact of artificial protein interactions on fitness. We engineered 44 yeast strains each expressing a tyrosine kinase, and quantitatively analysed their phosphoproteomes. This analysis resulted in ~30,000 phosphosites mapping to ~3,500 proteins. Examination of the fitness costs in each strain revealed a strong correlation between the number of spurious pY sites and decreased growth. Moreover, the analysis of pY effects on protein structure and on protein function revealed over 1000 pY events that we predict to be deleterious. However, we also find that a large number of the spurious pY sites have a negligible effect on fitness, possibly because of their low stoichiometry. This result is consistent with our evolutionary analyses demonstrating a lack of phosphotyrosine counter-selection in species with bona fide tyrosine kinases. Taken together, our results suggest that, alongside the risk for toxicity, the cell can tolerate a large degree of non-functional crosstalk as interaction networks evolve.
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Affiliation(s)
- David Bradley
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
- Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Québec, QC, Canada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université du Québec à Montréal, Montréal, QC, Canada
- Université Laval Big Data Research Center (BDRC_UL), Québec, QC, Canada
- Department of Biology, Université Laval, Québec, QC, Canada
| | - Alexander Hogrebe
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Rohan Dandage
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
- Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Québec, QC, Canada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université du Québec à Montréal, Montréal, QC, Canada
- Université Laval Big Data Research Center (BDRC_UL), Québec, QC, Canada
- Department of Biology, Université Laval, Québec, QC, Canada
| | - Alexandre K Dubé
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
- Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Québec, QC, Canada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université du Québec à Montréal, Montréal, QC, Canada
- Université Laval Big Data Research Center (BDRC_UL), Québec, QC, Canada
- Department of Biology, Université Laval, Québec, QC, Canada
| | - Mario Leutert
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
| | - Ugo Dionne
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
- Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Québec, QC, Canada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université du Québec à Montréal, Montréal, QC, Canada
- Université Laval Big Data Research Center (BDRC_UL), Québec, QC, Canada
- Department of Biology, Université Laval, Québec, QC, Canada
| | - Alexis Chang
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Judit Villén
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Christian R Landry
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
- Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Québec, QC, Canada
- Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université du Québec à Montréal, Montréal, QC, Canada
- Université Laval Big Data Research Center (BDRC_UL), Québec, QC, Canada
- Department of Biology, Université Laval, Québec, QC, Canada
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21
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Wright SC, Motso A, Koutsilieri S, Beusch CM, Sabatier P, Berghella A, Blondel-Tepaz É, Mangenot K, Pittarokoilis I, Sismanoglou DC, Le Gouill C, Olsen JV, Zubarev RA, Lambert NA, Hauser AS, Bouvier M, Lauschke VM. GLP-1R signaling neighborhoods associate with the susceptibility to adverse drug reactions of incretin mimetics. Nat Commun 2023; 14:6243. [PMID: 37813859 PMCID: PMC10562414 DOI: 10.1038/s41467-023-41893-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 09/19/2023] [Indexed: 10/11/2023] Open
Abstract
G protein-coupled receptors are important drug targets that engage and activate signaling transducers in multiple cellular compartments. Delineating therapeutic signaling from signaling associated with adverse events is an important step towards rational drug design. The glucagon-like peptide-1 receptor (GLP-1R) is a validated target for the treatment of diabetes and obesity, but drugs that target this receptor are a frequent cause of adverse events. Using recently developed biosensors, we explored the ability of GLP-1R to activate 15 pathways in 4 cellular compartments and demonstrate that modifications aimed at improving the therapeutic potential of GLP-1R agonists greatly influence compound efficacy, potency, and safety in a pathway- and compartment-selective manner. These findings, together with comparative structure analysis, time-lapse microscopy, and phosphoproteomics, reveal unique signaling signatures for GLP-1R agonists at the level of receptor conformation, functional selectivity, and location bias, thus associating signaling neighborhoods with functionally distinct cellular outcomes and clinical consequences.
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Affiliation(s)
- Shane C Wright
- Department of Physiology & Pharmacology, Karolinska Institutet, Stockholm, Sweden.
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, H3T 1J4, Canada.
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC, H3T 1J4, Canada.
| | - Aikaterini Motso
- Department of Physiology & Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Stefania Koutsilieri
- Department of Physiology & Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Christian M Beusch
- Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, 17177, Sweden
| | - Pierre Sabatier
- Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, 17177, Sweden
- Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
- Department of Surgical Sciences, Uppsala University, Uppsala, 75185, Sweden
| | - Alessandro Berghella
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Faculty of Bioscience and Agro-Food and Environmental Technology, University of Teramo, Teramo, 64100, Italy
| | - Élodie Blondel-Tepaz
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, H3T 1J4, Canada
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC, H3T 1J4, Canada
| | - Kimberley Mangenot
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, H3T 1J4, Canada
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC, H3T 1J4, Canada
| | | | | | - Christian Le Gouill
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, H3T 1J4, Canada
| | - Jesper V Olsen
- Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Roman A Zubarev
- Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, 17177, Sweden
- Department of Pharmacological & Technological Chemistry, I.M. Sechenov First Moscow State Medical University, Moscow, 119146, Russia
- The National Medical Research Center for Endocrinology, Moscow, 115478, Russia
| | - Nevin A Lambert
- Department of Pharmacology and Toxicology, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA
| | - Alexander S Hauser
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Michel Bouvier
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, H3T 1J4, Canada.
| | - Volker M Lauschke
- Department of Physiology & Pharmacology, Karolinska Institutet, Stockholm, Sweden.
- Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany.
- University of Tübingen, Tübingen, Germany.
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22
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Searle BC, Chien A, Koller A, Hawke D, Herren AW, Kim Kim J, Lee KA, Leib RD, Nelson AJ, Patel P, Ren JM, Stemmer PM, Zhu Y, Neely BA, Patel B. A Multipathway Phosphopeptide Standard for Rapid Phosphoproteomics Assay Development. Mol Cell Proteomics 2023; 22:100639. [PMID: 37657519 PMCID: PMC10561125 DOI: 10.1016/j.mcpro.2023.100639] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 08/22/2023] [Accepted: 08/24/2023] [Indexed: 09/03/2023] Open
Abstract
Recent advances in methodology have made phosphopeptide analysis a tractable problem for many proteomics researchers. There are now a wide variety of robust and accessible enrichment strategies to generate phosphoproteomes while free or inexpensive software tools for quantitation and site localization have simplified phosphoproteome analysis workflow tremendously. As a research group under the Association for Biomolecular Resource Facilities umbrella, the Proteomics Standards Research Group has worked to develop a multipathway phosphopeptide standard based on a mixture of heavy-labeled phosphopeptides designed to enable researchers to rapidly develop assays. This mixture contains 131 mass spectrometry vetted phosphopeptides specifically chosen to cover as many known biologically interesting phosphosites as possible from seven different signaling networks: AMPK signaling, death and apoptosis signaling, ErbB signaling, insulin/insulin-like growth factor-1 signaling, mTOR signaling, PI3K/AKT signaling, and stress (p38/SAPK/JNK) signaling. Here, we describe a characterization of this mixture spiked into a HeLa tryptic digest stimulated with both epidermal growth factor and insulin-like growth factor-1 to activate the MAPK and PI3K/AKT/mTOR pathways. We further demonstrate a comparison of phosphoproteomic profiling of HeLa performed independently in five labs using this phosphopeptide mixture with data-independent acquisition. Despite different experimental and instrumentation processes, we found that labs could produce reproducible, harmonized datasets by reporting measurements as ratios to the standard, while intensity measurements showed lower consistency between labs even after normalization. Our results suggest that widely available, biologically relevant phosphopeptide standards can act as a quantitative "yardstick" across laboratories and sample preparations enabling experimental designs larger than a single laboratory can perform. Raw data files are publicly available in the MassIVE dataset MSV000090564.
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Affiliation(s)
- Brian C Searle
- Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio, USA; Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio, USA.
| | - Allis Chien
- Mass Spectrometry Center, Stanford University, Stanford, California, USA
| | | | | | - Anthony W Herren
- UC Davis Genome Center, Proteomics Core, University of California Davis, Davis California, USA
| | - Jenny Kim Kim
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York, USA
| | - Kimberly A Lee
- Cell Signaling Technology, Inc, Danvers, Massachusetts, USA
| | - Ryan D Leib
- Mass Spectrometry Center, Stanford University, Stanford, California, USA
| | | | - Purvi Patel
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York, USA
| | - Jian Min Ren
- Cell Signaling Technology, Inc, Danvers, Massachusetts, USA
| | - Paul M Stemmer
- Department of Pharmaceutical Sciences, Wayne State University, Detroit, Michigan, USA
| | - Yiying Zhu
- Cell Signaling Technology, Inc, Danvers, Massachusetts, USA
| | - Benjamin A Neely
- National Institute of Standards and Technology, Charleston, South Carolina, USA
| | - Bhavin Patel
- Thermo Fisher Scientific, Rockford, Illinois, USA
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23
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Bossart J, Rippl A, Barton Alston AE, Flühmann B, Digigow R, Buljan M, Ayala-Nunez V, Wick P. Uncovering the dynamics of cellular responses induced by iron-carbohydrate complexes in human macrophages using quantitative proteomics and phosphoproteomics. Biomed Pharmacother 2023; 166:115404. [PMID: 37657262 DOI: 10.1016/j.biopha.2023.115404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 08/22/2023] [Accepted: 08/28/2023] [Indexed: 09/03/2023] Open
Abstract
Iron-carbohydrate complexes are widely used to treat iron deficiencies. Macrophages play a crucial role in the uptake and fate of these nanomedicines, however, how complexed iron carbohydrates are taken up and metabolized by macrophages is still not fully understood. Using a (phospho-)proteomics approach, we assessed differences in protein expression and phosphorylation in M2 macrophages triggered by iron sucrose (IS). Our results show that IS alters the expression of multiple receptors, indicative of a complex entry mechanism. Besides, IS induced an increase in intracellular ferritin, the loss of M2 polarization, protective mechanisms against ferroptosis, and an autophagic response. These data indicate that macrophages can use IS as a source of iron for its storage and later release, however, the excess of iron can cause oxidative stress, which can be successfully regulated by the cells. When comparing IS with ferric carboxymaltose (FCM) and iron isomaltoside-1000 (IIM), complexes with a higher carbohydrate ligand stability, we observed that FCM and IIM are metabolized at a slower rate, and trigger M2 polarization loss to a lower extent. These results indicate that the surface characteristics of the iron-carbohydrate complexes may influence the cell responses. Our data show that the application of (phospho-)proteomics can lead to a better understanding of metabolic processes, including the uptake, biodegradation and bioavailability of nanomedicines.
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Affiliation(s)
- Jonas Bossart
- Empa, Swiss Federal Laboratories for Materials Science and Technology, Particles-Biology Interactions Laboratory, CH-9014 St. Gallen, Switzerland; SIB, Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland; ETH Zurich, Department of Health Sciences and Technology (D-HEST), CH-8093 Zurich, Switzerland
| | - Alexandra Rippl
- Empa, Swiss Federal Laboratories for Materials Science and Technology, Particles-Biology Interactions Laboratory, CH-9014 St. Gallen, Switzerland
| | | | | | | | - Marija Buljan
- Empa, Swiss Federal Laboratories for Materials Science and Technology, Particles-Biology Interactions Laboratory, CH-9014 St. Gallen, Switzerland; SIB, Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Vanesa Ayala-Nunez
- Empa, Swiss Federal Laboratories for Materials Science and Technology, Particles-Biology Interactions Laboratory, CH-9014 St. Gallen, Switzerland.
| | - Peter Wick
- Empa, Swiss Federal Laboratories for Materials Science and Technology, Particles-Biology Interactions Laboratory, CH-9014 St. Gallen, Switzerland.
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Daszkowska-Golec A, Mehta D, Uhrig RG, Brąszewska A, Novak O, Fontana IM, Melzer M, Płociniczak T, Marzec M. Multi-omics insights into the positive role of strigolactone perception in barley drought response. BMC PLANT BIOLOGY 2023; 23:445. [PMID: 37735356 PMCID: PMC10515045 DOI: 10.1186/s12870-023-04450-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 09/08/2023] [Indexed: 09/23/2023]
Abstract
BACKGROUND Drought is a major environmental stress that affects crop productivity worldwide. Although previous research demonstrated links between strigolactones (SLs) and drought, here we used barley (Hordeum vulgare) SL-insensitive mutant hvd14 (dwarf14) to scrutinize the SL-dependent mechanisms associated with water deficit response. RESULTS We have employed a combination of transcriptomics, proteomics, phytohormonomics analyses, and physiological data to unravel differences between wild-type and hvd14 plants under drought. Our research revealed that drought sensitivity of hvd14 is related to weaker induction of abscisic acid-responsive genes/proteins, lower jasmonic acid content, higher reactive oxygen species content, and lower wax biosynthetic and deposition mechanisms than wild-type plants. In addition, we identified a set of transcription factors (TFs) that are exclusively drought-induced in the wild-type barley. CONCLUSIONS Critically, we resolved a comprehensive series of interactions between the drought-induced barley transcriptome and proteome responses, allowing us to understand the profound effects of SLs in alleviating water-limiting conditions. Several new avenues have opened for developing barley more resilient to drought through the information provided. Moreover, our study contributes to a better understanding of the complex interplay between genes, proteins, and hormones in response to drought, and underscores the importance of a multidisciplinary approach to studying plant stress response mechanisms.
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Affiliation(s)
- Agata Daszkowska-Golec
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Jagiellonska 28, 40-032, Katowice, Poland
| | - Devang Mehta
- Department of Biological Sciences, University of Alberta, 11455 Saskatchewan Drive, Edmonton, AB, T6G 2E9, Canada
| | - R Glen Uhrig
- Department of Biological Sciences, University of Alberta, 11455 Saskatchewan Drive, Edmonton, AB, T6G 2E9, Canada
| | - Agnieszka Brąszewska
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Jagiellonska 28, 40-032, Katowice, Poland
| | - Ondrej Novak
- Laboratory of Growth Regulators, Faculty of Science, Palacký University & Institute of Experimental Botany, The Czech Academy of Sciences, Olomouc, Czech Republic
| | - Irene M Fontana
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Seeland, 06466, Gatersleben, OT, Germany
| | - Michael Melzer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Seeland, 06466, Gatersleben, OT, Germany
| | - Tomasz Płociniczak
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Jagiellonska 28, 40-032, Katowice, Poland
| | - Marek Marzec
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Jagiellonska 28, 40-032, Katowice, Poland.
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25
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Krumm J, Petrova E, Lechner S, Mergner J, Boehm HH, Prestipino A, Steinbrunn D, Deline ML, Koetzner L, Schindler C, Helming L, Fromme T, Klingenspor M, Hahne H, Pieck JC, Kuster B. High-Throughput Screening and Proteomic Characterization of Compounds Targeting Myeloid-Derived Suppressor Cells. Mol Cell Proteomics 2023; 22:100632. [PMID: 37586548 PMCID: PMC10518717 DOI: 10.1016/j.mcpro.2023.100632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 08/09/2023] [Accepted: 08/11/2023] [Indexed: 08/18/2023] Open
Abstract
Myeloid-derived suppressor cells (MDSC) are a heterogeneous cell population of incompletely differentiated immune cells. They are known to suppress T cell activity and are implicated in multiple chronic diseases, which make them an attractive cell population for drug discovery. Here, we characterized the baseline proteomes and phospho-proteomes of mouse MDSC differentiated from a progenitor cell line to a depth of 7000 proteins and phosphorylation sites. We also validated the cellular system for drug discovery by recapitulating and identifying known and novel molecular responses to the well-studied MDSC drugs entinostat and mocetinostat. We established a high-throughput drug screening platform using a MDSC/T cell coculture system and assessed the effects of ∼21,000 small molecule compounds on T cell proliferation and IFN-γ secretion to identify novel MDSC modulator. The most promising candidates were validated in a human MDSC system, and subsequent proteomic experiments showed significant upregulation of several proteins associated with the reduction of reactive oxygen species (ROS). Proteome-wide solvent-induced protein stability assays identified Acyp1 and Cd74 as potential targets, and the ROS-reducing drug phenotype was validated by measuring ROS levels in cells in response to compound, suggesting a potential mode of action. We anticipate that the data and chemical tools developed in this study will be valuable for further research on MDSC and related drug discovery.
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Affiliation(s)
- Johannes Krumm
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Elissaveta Petrova
- Global Research & Development, Discovery and Development Technologies, Discovery Pharmacology, Healthcare Business of Merck KGaA, Darmstadt, Germany
| | - Severin Lechner
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Julia Mergner
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany; Bavarian Center for Biomolecular Mass Spectrometry at Klinikum rechts der Isar (BayBioMS@MRI), Technical University of Munich, Munich, Germany
| | - Hans-Henning Boehm
- Global Research & Development, TIP-Oncology & Immunooncology, Myeloid Cell Research, Healthcare Business of Merck KGaA, Darmstadt, Germany
| | - Alessandro Prestipino
- Global Research & Development, Discovery and Development Technologies, Discovery Pharmacology, Healthcare Business of Merck KGaA, Darmstadt, Germany
| | | | - Marshall L Deline
- Chair of Molecular Nutritional Medicine, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Lisa Koetzner
- Global Research & Development, Discovery and Development Technologies, Global Medicinal Chemistry, Healthcare Business of Merck KGaA, Darmstadt, Germany
| | - Christina Schindler
- Global Research & Development, Discovery Technologies, Computational Chemistry & Biologics, Healthcare Business of Merck KGaA, Darmstadt, Germany
| | - Laura Helming
- Global Research & Development, TIP-Oncology & Immunooncology, Myeloid Cell Research, Healthcare Business of Merck KGaA, Darmstadt, Germany
| | - Tobias Fromme
- Chair of Molecular Nutritional Medicine, TUM School of Life Sciences, Technical University of Munich, Freising, Germany; Else Kröner Fresenius Center for Nutritional Medicine, Technical University of Munich, Freising, Germany; ZIEL Institute for Food & Health, Technical University of Munich, Freising, Germany
| | - Martin Klingenspor
- Chair of Molecular Nutritional Medicine, TUM School of Life Sciences, Technical University of Munich, Freising, Germany; Else Kröner Fresenius Center for Nutritional Medicine, Technical University of Munich, Freising, Germany; ZIEL Institute for Food & Health, Technical University of Munich, Freising, Germany
| | | | - Jan-Carsten Pieck
- Global Research & Development, Discovery and Development Technologies, Discovery Pharmacology, Healthcare Business of Merck KGaA, Darmstadt, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany; Bavarian Biomolecular Mass Spectrometry Center (BayBioMS), Technical University of Munich, Freising, Germany.
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26
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Birhanu AG. Mass spectrometry-based proteomics as an emerging tool in clinical laboratories. Clin Proteomics 2023; 20:32. [PMID: 37633929 PMCID: PMC10464495 DOI: 10.1186/s12014-023-09424-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 08/03/2023] [Indexed: 08/28/2023] Open
Abstract
Mass spectrometry (MS)-based proteomics have been increasingly implemented in various disciplines of laboratory medicine to identify and quantify biomolecules in a variety of biological specimens. MS-based proteomics is continuously expanding and widely applied in biomarker discovery for early detection, prognosis and markers for treatment response prediction and monitoring. Furthermore, making these advanced tests more accessible and affordable will have the greatest healthcare benefit.This review article highlights the new paradigms MS-based clinical proteomics has created in microbiology laboratories, cancer research and diagnosis of metabolic disorders. The technique is preferred over conventional methods in disease detection and therapy monitoring for its combined advantages in multiplexing capacity, remarkable analytical specificity and sensitivity and low turnaround time.Despite the achievements in the development and adoption of a number of MS-based clinical proteomics practices, more are expected to undergo transition from bench to bedside in the near future. The review provides insights from early trials and recent progresses (mainly covering literature from the NCBI database) in the application of proteomics in clinical laboratories.
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27
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Car I, Dittmann A, Vasieva O, Bočkor L, Grbčić P, Piteša N, Klobučar M, Kraljević Pavelić S, Sedić M. Ezrin Inhibition Overcomes Acquired Resistance to Vemurafenib in BRAFV600E-Mutated Colon Cancer and Melanoma Cells In Vitro. Int J Mol Sci 2023; 24:12906. [PMID: 37629086 PMCID: PMC10454476 DOI: 10.3390/ijms241612906] [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: 06/07/2023] [Revised: 08/14/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023] Open
Abstract
Despite the advancements in targeted therapy for BRAFV600E-mutated metastatic colorectal cancer (mCRC), the development of resistance to BRAFV600E inhibition limits the response rate and durability of the treatment. Better understanding of the resistance mechanisms to BRAF inhibitors will facilitate the design of novel pharmacological strategies for BRAF-mutated mCRC. The aim of this study was to identify novel protein candidates involved in acquired resistance to BRAFV600E inhibitor vemurafenib in BRAFV600E-mutated colon cancer cells using an integrated proteomics approach. Bioinformatic analysis of obtained proteomics data indicated actin-cytoskeleton linker protein ezrin as a highly ranked protein significantly associated with vemurafenib resistance whose overexpression in the resistant cells was additionally confirmed at the gene and protein level. Ezrin inhibition by NSC305787 increased anti-proliferative and pro-apoptotic effects of vemurafenib in the resistant cells in an additive manner, which was accompanied by downregulation of CD44 expression and inhibition of AKT/c-Myc activities. We also detected an increased ezrin expression in vemurafenib-resistant melanoma cells harbouring the BRAFV600E mutation. Importantly, ezrin inhibition potentiated anti-proliferative and pro-apoptotic effects of vemurafenib in the resistant melanoma cells in a synergistic manner. Altogether, our study suggests a role of ezrin in acquired resistance to vemurafenib in colon cancer and melanoma cells carrying the BRAFV600E mutation and supports further pre-clinical and clinical studies to explore the benefits of combined BRAF inhibitors and actin-targeting drugs as a potential therapeutic approach for BRAFV600E-mutated cancers.
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Affiliation(s)
- Iris Car
- Centre for Applied Bioanthropology, Institute for Anthropological Research, Ljudevita Gaja 32, 10000 Zagreb, Croatia; (I.C.); (L.B.); (M.K.)
| | - Antje Dittmann
- Functional Genomics Center Zurich, ETH Zurich, Winterthurerstr. 190, Y59 H38, 8057 Zurich, Switzerland;
| | - Olga Vasieva
- INGENET Ltd., 27 Market Street, Hoylake, Wirral CH47 2BG, UK;
| | - Luka Bočkor
- Centre for Applied Bioanthropology, Institute for Anthropological Research, Ljudevita Gaja 32, 10000 Zagreb, Croatia; (I.C.); (L.B.); (M.K.)
| | - Petra Grbčić
- Faculty of Medicine, Juraj Dobrila University of Pula, Zagrebačka ul. 30, 52100 Pula, Croatia;
| | - Nikolina Piteša
- Division of Molecular Medicine, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia;
| | - Marko Klobučar
- Centre for Applied Bioanthropology, Institute for Anthropological Research, Ljudevita Gaja 32, 10000 Zagreb, Croatia; (I.C.); (L.B.); (M.K.)
| | | | - Mirela Sedić
- Centre for Applied Bioanthropology, Institute for Anthropological Research, Ljudevita Gaja 32, 10000 Zagreb, Croatia; (I.C.); (L.B.); (M.K.)
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28
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Zittlau K, Nashier P, Cavarischia-Rega C, Macek B, Spät P, Nalpas N. Recent progress in quantitative phosphoproteomics. Expert Rev Proteomics 2023; 20:469-482. [PMID: 38116637 DOI: 10.1080/14789450.2023.2295872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 12/12/2023] [Indexed: 12/21/2023]
Abstract
INTRODUCTION Protein phosphorylation is a critical post-translational modification involved in the regulation of numerous cellular processes from signal transduction to modulation of enzyme activities. Knowledge of dynamic changes of phosphorylation levels during biological processes, under various treatments or between healthy and disease models is fundamental for understanding the role of each phosphorylation event. Thereby, LC-MS/MS based technologies in combination with quantitative proteomics strategies evolved as a powerful strategy to investigate the function of individual protein phosphorylation events. AREAS COVERED State-of-the-art labeling techniques including stable isotope and isobaric labeling provide precise and accurate quantification of phosphorylation events. Here, we review the strengths and limitations of recent quantification methods and provide examples based on current studies, how quantitative phosphoproteomics can be further optimized for enhanced analytic depth, dynamic range, site localization, and data integrity. Specifically, reducing the input material demands is key to a broader implementation of quantitative phosphoproteomics, not least for clinical samples. EXPERT OPINION Despite quantitative phosphoproteomics is one of the most thriving fields in the proteomics world, many challenges still have to be overcome to facilitate even deeper and more comprehensive analyses as required in the current research, especially at single cell levels and in clinical diagnostics.
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Affiliation(s)
- Katharina Zittlau
- Quantitative Proteomics, Interfaculty Institute of Cell Biology, University of Tuebingen, Tuebingen , Germany
| | - Payal Nashier
- Quantitative Proteomics, Interfaculty Institute of Cell Biology, University of Tuebingen, Tuebingen , Germany
| | - Claudia Cavarischia-Rega
- Quantitative Proteomics, Interfaculty Institute of Cell Biology, University of Tuebingen, Tuebingen , Germany
| | - Boris Macek
- Quantitative Proteomics, Interfaculty Institute of Cell Biology, University of Tuebingen, Tuebingen , Germany
| | - Philipp Spät
- Quantitative Proteomics, Interfaculty Institute of Cell Biology, University of Tuebingen, Tuebingen , Germany
| | - Nicolas Nalpas
- Quantitative Proteomics, Interfaculty Institute of Cell Biology, University of Tuebingen, Tuebingen , Germany
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29
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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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30
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Car I, Dittmann A, Klobučar M, Grbčić P, Kraljević Pavelić S, Sedić M. Secretome Screening of BRAFV600E-Mutated Colon Cancer Cells Resistant to Vemurafenib. BIOLOGY 2023; 12:biology12040608. [PMID: 37106808 PMCID: PMC10136293 DOI: 10.3390/biology12040608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 04/11/2023] [Accepted: 04/14/2023] [Indexed: 04/29/2023]
Abstract
Patients with metastatic colorectal cancer (mCRC) carrying BRAFV600E mutation have worse response to chemotherapy and poor prognosis. The BRAFV600E inhibitor vemurafenib has shown modest efficacy as monotherapy in BRAF-mutated mCRC due to the development of resistance. The aim of this study was to conduct a comparative proteomics profiling of the secretome from vemurafenib-sensitive vs. -resistant colon cancer cells harboring BRAFV600E mutation in order to identify specific secretory features potentially associated with changes in the resistant cells' phenotype. Towards this aim, we employed two complementary proteomics approaches including two-dimensional gel electrophoresis coupled with MALDI-TOF/TOF mass spectrometry and label-free quantitative LC-MS/MS analysis. Obtained results pointed to aberrant regulation of DNA replication and endoplasmic reticulum stress as the major secretome features associated with chemoresistant phenotype. Accordingly, two proteins implicated in these processes including RPA1 and HSPA5/GRP78 were discussed in more details in the context of biological networks and their importance as potential secretome targets for further functional and clinical evaluation. Expression patterns of RPA1 and HSPA5/GRP78 in tumor tissues from colon cancer patients were also found in additional in silico analyses to be associated with BRAFV600E mutation status, which opens the possibility to extrapolate our findings and their clinical implication to other solid tumors harboring BRAFV600E mutation, such as melanoma.
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Affiliation(s)
- Iris Car
- Centre for Applied Bioanthropology, Institute for Anthropological Research, Ljudevita Gaja 32, 10000 Zagreb, Croatia
| | - Antje Dittmann
- Functional Genomics Center Zurich, ETH Zurich, Winterthurerstr. 190, Y59 H38, 8057 Zurich, Switzerland
| | - Marko Klobučar
- Centre for Applied Bioanthropology, Institute for Anthropological Research, Ljudevita Gaja 32, 10000 Zagreb, Croatia
| | - Petra Grbčić
- Faculty of Medicine, Juraj Dobrila University of Pula, Zagrebačka ul. 30, 52100 Pula, Croatia
| | | | - Mirela Sedić
- Centre for Applied Bioanthropology, Institute for Anthropological Research, Ljudevita Gaja 32, 10000 Zagreb, Croatia
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31
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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: 26] [Impact Index Per Article: 26.0] [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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32
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Franciosa G, Locard-Paulet M, Jensen LJ, Olsen JV. Recent advances in kinase signaling network profiling by mass spectrometry. Curr Opin Chem Biol 2023; 73:102260. [PMID: 36657259 DOI: 10.1016/j.cbpa.2022.102260] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 12/13/2022] [Accepted: 12/14/2022] [Indexed: 01/19/2023]
Abstract
Mass spectrometry-based phosphoproteomics is currently the leading methodology for the study of global kinase signaling. The scientific community is continuously releasing technological improvements for sensitive and fast identification of phosphopeptides, and their accurate quantification. To interpret large-scale phosphoproteomics data, numerous bioinformatic resources are available that help understanding kinase network functional role in biological systems upon perturbation. Some of these resources are databases of phosphorylation sites, protein kinases and phosphatases; others are bioinformatic algorithms to infer kinase activity, predict phosphosite functional relevance and visualize kinase signaling networks. In this review, we present the latest experimental and bioinformatic tools to profile protein kinase signaling networks and provide examples of their application in biomedicine.
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Affiliation(s)
- Giulia Franciosa
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Marie Locard-Paulet
- Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lars J Jensen
- Disease Systems Biology Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jesper V Olsen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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33
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Vera-Montecinos A, Rodríguez-Mias R, Vila È, Villén J, Ramos B. Analysis of networks in the dorsolateral prefrontal cortex in chronic schizophrenia: Relevance of altered immune response. Front Pharmacol 2023; 14:1003557. [PMID: 37033658 PMCID: PMC10076656 DOI: 10.3389/fphar.2023.1003557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 03/09/2023] [Indexed: 04/11/2023] Open
Abstract
The dorsolateral prefrontal cortex (DLPFC) has a crucial role in cognitive functioning and negative symptoms in schizophrenia. However, limited information of altered protein networks is available in this region in schizophrenia. We performed a proteomic analysis using single-shot liquid chromatography-tandem mass spectrometry of grey matter of postmortem DLPFC in chronic schizophrenia subjects (n = 20) and unaffected subjects (n = 20) followed by bioinformatic analysis to identify altered protein networks in schizophrenia (PXD024939 identifier in ProteomeXchange repository). Our results displayed a proteome profile in the DLPFC of 1989 proteins. 43 proteins were found significantly altered in schizophrenia. Analysis of this panel showed an enrichment of biological processes implicated in vesicle-mediated transport, processing and antigen presentation via MHC class II, intracellular transport and selenium metabolism. The enriched identified pathways were MHC class II antigen presentation, vesicle-mediated transport, Golgi ER retrograde transport, Nef mediated CD8 downregulation and the immune system. All these enriched categories were found to be downregulated. Furthermore, our network analyses showed crosstalk between proteins involved in MHC class II antigen presentation, membrane trafficking, Golgi-to-ER retrograde transport, Nef-mediated CD8 downregulation and the immune system with only one module built by 13 proteins. RAB7A showed eight interactions with proteins of all these pathways. Our results provide an altered molecular network involved in immune response in the DLPFC in schizophrenia with a central role of RAB7A. These results suggest that RAB7A or other proteins of this network could be potential targets for novel pharmacological strategies in schizophrenia for improving cognitive and negative symptoms.
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Affiliation(s)
- América Vera-Montecinos
- Psiquiatria Molecular, Parc Sanitari Sant Joan de Déu, Institut de Recerca Sant Joan de Déu, Sant Boi de Llobregat, Spain
| | - Ricard Rodríguez-Mias
- Department of Genome Sciences, School of Medicine, University of Washington, Seattle, WA, United States
| | - Èlia Vila
- Psiquiatria Molecular, Parc Sanitari Sant Joan de Déu, Institut de Recerca Sant Joan de Déu, Sant Boi de Llobregat, Spain
| | - Judit Villén
- Department of Genome Sciences, School of Medicine, University of Washington, Seattle, WA, United States
| | - Belén Ramos
- Psiquiatria Molecular, Parc Sanitari Sant Joan de Déu, Institut de Recerca Sant Joan de Déu, Sant Boi de Llobregat, Spain
- Centro de Investigación Biomédica en Red de Salud Mental, CIBERSAM (Biomedical Network Research Center of Mental Health), Ministry of Economy, Industry and Competitiveness, Institute of Health Carlos III, Madrid, Spain
- Department de Bioquímica i Biología Molecular, Facultat de Medicina, Universitat Autònoma de Barcelona, Barcelona, Spain
- Facultat de Medicina, Universitat de Vic-Universitat Central de Catalunya, Vic, Spain
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34
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Boyd A, Luu I, Mehta D, Myers SP, Stewart CB, Shivakumar KR, Snihur KN, Alessi DS, Rodriguez Gallo MC, Veilleux H, Wiltse ME, Borch T, Uhrig RG, Blewett TA. Persisting Effects in Daphnia magna Following an Acute Exposure to Flowback and Produced Waters from the Montney Formation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:2380-2392. [PMID: 36724135 DOI: 10.1021/acs.est.2c07441] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Hydraulic fracturing extracts oil and gas through the injection of water and proppants into subterranean formations. These injected fluids mix with the host rock formation and return to the surface as a complex wastewater containing salts, metals, and organic compounds, termed flowback and produced water (FPW). Previous research indicates that FPW is toxic to Daphnia magna (D. magna), impairing reproduction, molting, and maturation time; however, recovery from FPW has not been extensively studied. Species unable to recover have drastic impacts on populations on the ecological scale; thus, this study sought to understand if recovery from an acute 48 h FPW exposure was possible in the freshwater invertebrate, D. magna by using a combination of physiological and molecular analyses. FPW (0.75%) reduced reproduction by 30% and survivorship to 32% compared to controls. System-level quantitative proteomic analyses demonstrate extensive perturbation of metabolism and protein transport in both 0.25 and 0.75% FPW treatments after a 48 h FPW exposure. Collectively, our data indicate that D. magna are unable to recover from acute 48 h exposures to ≥0.25% FPW, as evidence of toxicity persists for at least 19 days post-exposure. This study highlights the importance of considering persisting effects following FPW remediation when modeling potential spill scenarios.
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Affiliation(s)
- Aaron Boyd
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
| | - Ivy Luu
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
| | - Devang Mehta
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
| | - Sunil P Myers
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
| | - Connor B Stewart
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
| | - Karthik R Shivakumar
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, Alberta T6G 2E3, Canada
| | - Katherine N Snihur
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, Alberta T6G 2E3, Canada
| | - Daniel S Alessi
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, Alberta T6G 2E3, Canada
| | | | - Heather Veilleux
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
| | - Marin E Wiltse
- Department of Soil and Crop Sciences and Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Thomas Borch
- Department of Soil and Crop Sciences and Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
| | - R Glen Uhrig
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
| | - Tamzin A Blewett
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
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35
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Zhang L, Wu F, Fan C, Huang S, Ma Y, Chen S, Zhang J, Jiang H. Quantitative phosphoproteomic analysis of mice with liver fibrosis by DIA mass spectrometry analysis with PRM verification. J Proteomics 2023; 271:104768. [PMID: 36336261 DOI: 10.1016/j.jprot.2022.104768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 10/21/2022] [Accepted: 10/24/2022] [Indexed: 11/06/2022]
Abstract
Liver fibrosis (LF), commonly associated with chronic liver diseases, is a major public health problem worldwide. Protein phosphorylation is not only an important form of protein modification in organisms but also the most important mechanism to regulate and control the activity and function of proteins, affecting the occurrence and development of many diseases. However, comprehensive phosphoproteomic profiling in LF has not been fully elucidated. In this study, data-independent acquisition (DIA) was used to analyse the phosphoproteomics of mice with LF. A total of 553 phosphopeptides (representing 440 phosphoproteins) had significant phosphorylation levels. Among these phosphoproteins, 49 were upregulated and 401 were downregulated, and 5 phosphoserine (P-Ser) motifs and 2 phosphothreonine (P-Thr) motifs were conserved in LF. GO and KEGG pathway enrichment analyses identified 769 significant GO terms and 49 significant KEGG pathways. Four phosphorylated proteins were selected for parallel reaction monitoring (PRM) verification, and the results were consistent with DIA data. Together, there were significantly different phosphoproteomic profiles in LF, suggesting that protein phosphorylation was related to the occurrence and progression of LF, which could pave the way for further investigation into the related regulatory mechanisms. SIGNIFICANCE: LF is a necessary stage in the development of chronic liver disease to liver cirrhosis and has attracted wide attention. To the best of our knowledge, there are few reports on the phosphorylated proteomics of LF. In this study, DIA and PRM techniques were used to study the liver tissue of mice induced by CCl4. The results showed that phosphorylation had a significant effect on the activity and function of proteins, and the PRM results were consistent with the trend observed in DIA analysis. This study will help to better reveal the relationship of phosphorylated proteins in LF and lay a foundation for further study of related regulatory mechanisms.
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Affiliation(s)
- Lili Zhang
- Experimental Center of Clinical Research, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China; School of Pharmacy, Anhui University of Chinese Medicine, Hefei, China.
| | - Furong Wu
- Department of Pharmacy, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
| | - Chang Fan
- Experimental Center of Clinical Research, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China; School of Pharmacy, Anhui University of Chinese Medicine, Hefei, China.
| | - Shaopeng Huang
- Experimental Center of Clinical Research, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China; School of Pharmacy, Anhui University of Chinese Medicine, Hefei, China.
| | - Yanzhen Ma
- Experimental Center of Clinical Research, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China; School of Pharmacy, Anhui University of Chinese Medicine, Hefei, China.
| | - Sen Chen
- Experimental Center of Clinical Research, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China; School of Pharmacy, Anhui University of Chinese Medicine, Hefei, China.
| | - Jiafu Zhang
- Department of Pharmacy, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China.
| | - Hui Jiang
- Experimental Center of Clinical Research, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China; School of Pharmacy, Anhui University of Chinese Medicine, Hefei, China.
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36
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Chang A, Leutert M, Rodriguez-Mias RA, Villén J. Automated Enrichment of Phosphotyrosine Peptides for High-Throughput Proteomics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.05.522335. [PMID: 36711935 PMCID: PMC9881991 DOI: 10.1101/2023.01.05.522335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Phosphotyrosine (pY) enrichment is critical for expanding 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 handles 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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37
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Cozma E, Rao M, Dusick M, Genereaux J, Rodriguez-Mias RA, Villén J, Brandl CJ, Berg MD. Anticodon sequence determines the impact of mistranslating tRNA Ala variants. RNA Biol 2023; 20:791-804. [PMID: 37776539 PMCID: PMC10543346 DOI: 10.1080/15476286.2023.2257471] [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] [Accepted: 08/31/2023] [Indexed: 10/02/2023] Open
Abstract
Transfer RNAs (tRNAs) maintain translation fidelity through accurate charging by their cognate aminoacyl-tRNA synthetase and codon:anticodon base pairing with the mRNA at the ribosome. Mistranslation occurs when an amino acid not specified by the genetic message is incorporated into proteins and has applications in biotechnology, therapeutics and is relevant to disease. Since the alanyl-tRNA synthetase uniquely recognizes a G3:U70 base pair in tRNAAla and the anticodon plays no role in charging, tRNAAla variants with anticodon mutations have the potential to mis-incorporate alanine. Here, we characterize the impact of the 60 non-alanine tRNAAla anticodon variants on the growth of Saccharomyces cerevisiae. Overall, 36 tRNAAla anticodon variants decreased growth in single- or multi-copy. Mass spectrometry analysis of the cellular proteome revealed that 52 of 57 anticodon variants, not decoding alanine or stop codons, induced mistranslation when on single-copy plasmids. Variants with G/C-rich anticodons resulted in larger growth deficits than A/U-rich variants. In most instances, synonymous anticodon variants impact growth differently, with anticodons containing U at base 34 being the least impactful. For anticodons generating the same amino acid substitution, reduced growth generally correlated with the abundance of detected mistranslation events. Differences in decoding specificity, even between synonymous anticodons, resulted in each tRNAAla variant mistranslating unique sets of peptides and proteins. We suggest that these differences in decoding specificity are also important in determining the impact of tRNAAla anticodon variants.
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Affiliation(s)
- Ecaterina Cozma
- Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada
| | - Megha Rao
- Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada
| | - Madison Dusick
- Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada
| | - Julie Genereaux
- Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada
| | | | - Judit Villén
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Christopher J. Brandl
- Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada
| | - Matthew D. Berg
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
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38
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Müller T, Cremonini MA, Kliewer G, Krijgsveld J. Automated Sample Preparation for Mass Spectrometry-Based Clinical Proteomics. Methods Mol Biol 2023; 2718:181-211. [PMID: 37665461 DOI: 10.1007/978-1-0716-3457-8_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Mass spectrometry (MS)-based proteomics is a rapidly maturing discipline, thus gaining momentum for routine molecular profiling of clinical specimens to improve disease classification, diagnostics, and therapy development. Yet, hurdles need to be overcome to enhance reproducibility in preanalytical sample processing, especially in large, quantity-limited sample cohorts. Therefore, automated sonication and single-pot solid-phase-enhanced sample preparation (autoSP3) was developed as a streamlined workflow that integrates all tasks from tissue lysis and protein extraction, protein cleanup, and proteolysis. It enables the concurrent processing of 96 clinical samples of any type (fresh-frozen or FFPE tissue, liquid biopsies, or cells) on an automated liquid handling platform, which can be directly interfaced to LC-MS for proteome analysis of clinical specimens with high sensitivity, high reproducibility, and short turn-around times.
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Affiliation(s)
- Torsten Müller
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg University, Medical Faculty, Heidelberg, Germany
| | | | - Georg Kliewer
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg University, Medical Faculty, Heidelberg, Germany
| | - Jeroen Krijgsveld
- German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Heidelberg University, Medical Faculty, Heidelberg, Germany.
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39
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Muraoka S, Hirano M, Isoyama J, Ishida M, Tomonaga T, Adachi J. Automated Proteomics Sample Preparation of Phosphatidylserine-Positive Extracellular Vesicles from Human Body Fluids. ACS OMEGA 2022; 7:41472-41479. [PMID: 36406491 PMCID: PMC9670285 DOI: 10.1021/acsomega.2c05244] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 10/24/2022] [Indexed: 06/16/2023]
Abstract
Extracellular vesicles (EVs) are ubiquitously secreted by almost every cell type and are present in all body fluids. Blood-derived EVs can be used as a promising source for biomarker monitoring in disease. EV proteomics is currently being analyzed in clinical specimens. However, their EV proteomics preparation methods are limited in throughput for human subjects. Here, we introduced a novel automated EV isolation and sample preparation method using a magnetic particle processing robot for automated 96-well processing of magnetic particles for EV proteomics analysis that can be started with a low volume of multiple clinical samples. The automation of EV purification reduced the coefficient of variation of protein quantification from 3.5 to 2.2% compared with manual purification, enabling the quantification of 1120 proteins in 1 h of MS analysis. This automated proteomics EV sample preparation is attractive for processing large cohort samples for biomarker development, validation, and routine testing.
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Affiliation(s)
- Satoshi Muraoka
- Laboratory
of Proteomics for Drug Discovery, Center for Drug Design Research, National Institute of Biomedical Innovation, Health
and Nutrition, Osaka 567-0085, Japan
- Laboratory
of Clinical and Analytical Chemistry, Collaborative Research Center
for Health and Medicine, National Institute
of Biomedical Innovation, Health and Nutrition, Osaka 567-0085, Japan
| | - Masayo Hirano
- Laboratory
of Proteomics for Drug Discovery, Center for Drug Design Research, National Institute of Biomedical Innovation, Health
and Nutrition, Osaka 567-0085, Japan
| | - Junko Isoyama
- Laboratory
of Proteomics for Drug Discovery, Center for Drug Design Research, National Institute of Biomedical Innovation, Health
and Nutrition, Osaka 567-0085, Japan
| | - Mimiko Ishida
- Laboratory
of Proteomics for Drug Discovery, Center for Drug Design Research, National Institute of Biomedical Innovation, Health
and Nutrition, Osaka 567-0085, Japan
| | - Takeshi Tomonaga
- Laboratory
of Proteomics for Drug Discovery, Center for Drug Design Research, National Institute of Biomedical Innovation, Health
and Nutrition, Osaka 567-0085, Japan
| | - Jun Adachi
- Laboratory
of Proteomics for Drug Discovery, Center for Drug Design Research, National Institute of Biomedical Innovation, Health
and Nutrition, Osaka 567-0085, Japan
- Laboratory
of Clinical and Analytical Chemistry, Collaborative Research Center
for Health and Medicine, National Institute
of Biomedical Innovation, Health and Nutrition, Osaka 567-0085, Japan
- Laboratory
of Proteomics and Drug Discovery, Graduate School of Pharmaceutical
Sciences, Kyoto University, Kyoto 606-8501, Japan
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40
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Coronary Artery Disease and Aortic Valve Stenosis: A Urine Proteomics Study. Int J Mol Sci 2022; 23:ijms232113579. [PMID: 36362368 PMCID: PMC9693565 DOI: 10.3390/ijms232113579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 10/28/2022] [Accepted: 10/30/2022] [Indexed: 11/09/2022] Open
Abstract
Coronary artery disease (CAD) and the frequently coexisting aortic valve stenosis (AVS) are heart diseases accounting for most cardiac surgeries. These share many risk factors, such as age, diabetes, hypertension, or obesity, and similar pathogenesis, including endothelial disruption, lipid and immune cell infiltration, inflammation, fibrosis, and calcification. Unsuspected CAD and AVS are sometimes detected opportunistically through echocardiography, coronary angiography, and magnetic resonance. Routine biomarkers for early detection of either of these atherosclerotic-rooted conditions would be important to anticipate the diagnosis. With a noninvasive collection, urine is appealing for biomarker assessment. We conducted a shotgun proteomics exploratory analysis of urine from 12 CAD and/or AVS patients and 11 controls to identify putative candidates to differentiate these diseases from healthy subjects. Among the top 20 most dysregulated proteins, TIMP1, MMP2 and vWF stood out, being at least 2.5× increased in patients with CAD/AVS and holding a central position in a network of protein-protein interactions. Moreover, their assessment in an independent cohort (19 CAD/AVS and 10 controls) evidenced strong correlations between urinary TIMP1 and vWF levels and a common cardiovascular risk factor - HDL (r = 0.59, p < 0.05, and r = 0.64, p < 0.01, respectively).
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41
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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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42
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Jensen ED, Deichmann M, Ma X, Vilandt RU, Schiesaro G, Rojek MB, Lengger B, Eliasson L, Vento JM, Durmusoglu D, Hovmand SP, Al'Abri I, Zhang J, Crook N, Jensen MK. Engineered cell differentiation and sexual reproduction in probiotic and mating yeasts. Nat Commun 2022; 13:6201. [PMID: 36261657 PMCID: PMC9582028 DOI: 10.1038/s41467-022-33961-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 10/10/2022] [Indexed: 12/24/2022] Open
Abstract
G protein-coupled receptors (GPCRs) enable cells to sense environmental cues and are indispensable for coordinating vital processes including quorum sensing, proliferation, and sexual reproduction. GPCRs comprise the largest class of cell surface receptors in eukaryotes, and for more than three decades the pheromone-induced mating pathway in baker's yeast Saccharomyces cerevisiae has served as a model for studying heterologous GPCRs (hGPCRs). Here we report transcriptome profiles following mating pathway activation in native and hGPCR-signaling yeast and use a model-guided approach to correlate gene expression to morphological changes. From this we demonstrate mating between haploid cells armed with hGPCRs and endogenous biosynthesis of their cognate ligands. Furthermore, we devise a ligand-free screening strategy for hGPCR compatibility with the yeast mating pathway and enable hGPCR-signaling in the probiotic yeast Saccharomyces boulardii. Combined, our findings enable new means to study mating, hGPCR-signaling, and cell-cell communication in a model eukaryote and yeast probiotics.
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Affiliation(s)
- Emil D Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs, Lyngby, Denmark.
| | - Marcus Deichmann
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Xin Ma
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Rikke U Vilandt
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Giovanni Schiesaro
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Marie B Rojek
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Bettina Lengger
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Line Eliasson
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Justin M Vento
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, 27695, USA
| | - Deniz Durmusoglu
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, 27695, USA
| | - Sandie P Hovmand
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Ibrahim Al'Abri
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, 27695, USA
| | - Jie Zhang
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Nathan Crook
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, 27695, USA
| | - Michael K Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs, Lyngby, Denmark.
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43
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Paulo JA. Isobaric labeling: Expanding the breadth, accuracy, depth, and diversity of sample multiplexing. Proteomics 2022; 22:e2200328. [PMID: 36089831 PMCID: PMC10777124 DOI: 10.1002/pmic.202200328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 08/25/2022] [Accepted: 08/26/2022] [Indexed: 11/10/2022]
Abstract
Isobaric labeling has rapidly become a predominant strategy for proteome-wide abundance measurements. Coupled to mass spectrometry, sample multiplexing techniques using isobaric labeling are unparalleled for profiling proteins and posttranslational modifications across multiple samples in a single experiment. Here, I highlight aspects of isobaric labeling in the context of expanding the breadth of multiplexing, improving quantitative accuracy and proteome depth, and developing a wide range of diverse applications. I underscore two facets that enhance quantitative accuracy and reproducibility, specifically the availability of quality control standards for isobaric labeling experiments and the evolution of data acquisition methods. I also emphasize the necessity for standardized methodologies, particularly for emerging high-throughput workflows. Future developments in sample multiplexing will further strengthen the importance of isobaric labeling for comprehensive proteome profiling.
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Affiliation(s)
- Joao A Paulo
- Department of Cell Biology, Blavatnik Institute at Harvard Medical School, Boston, Massachusetts, USA
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44
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Scandola S, Mehta D, Li Q, Rodriguez Gallo MC, Castillo B, Uhrig RG. Multi-omic analysis shows REVEILLE clock genes are involved in carbohydrate metabolism and proteasome function. PLANT PHYSIOLOGY 2022; 190:1005-1023. [PMID: 35670757 PMCID: PMC9516735 DOI: 10.1093/plphys/kiac269] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 05/12/2022] [Indexed: 06/01/2023]
Abstract
Plants are able to sense changes in their light environments, such as the onset of day and night, as well as anticipate these changes in order to adapt and survive. Central to this ability is the plant circadian clock, a molecular circuit that precisely orchestrates plant cell processes over the course of a day. REVEILLE (RVE) proteins are recently discovered members of the plant circadian circuitry that activate the evening complex and PSEUDO-RESPONSE REGULATOR genes to maintain regular circadian oscillation. The RVE8 protein and its two homologs, RVE 4 and 6 in Arabidopsis (Arabidopsis thaliana), have been shown to limit the length of the circadian period, with rve 4 6 8 triple-knockout plants possessing an elongated period along with increased leaf surface area, biomass, cell size, and delayed flowering relative to wild-type Col-0 plants. Here, using a multi-omics approach consisting of phenomics, transcriptomics, proteomics, and metabolomics we draw new connections between RVE8-like proteins and a number of core plant cell processes. In particular, we reveal that loss of RVE8-like proteins results in altered carbohydrate, organic acid, and lipid metabolism, including a starch excess phenotype at dawn. We further demonstrate that rve 4 6 8 plants have lower levels of 20S proteasome subunits and possess significantly reduced proteasome activity, potentially explaining the increase in cell-size observed in RVE8-like mutants. Overall, this robust, multi-omic dataset provides substantial insight into the far-reaching impact RVE8-like proteins have on the diel plant cell environment.
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Affiliation(s)
| | | | - Qiaomu Li
- Department of Biological Sciences, University of Alberta, Edmonton, Canada
| | | | - Brigo Castillo
- Department of Biological Sciences, University of Alberta, Edmonton, Canada
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45
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Johnston HE, Yadav K, Kirkpatrick JM, Biggs GS, Oxley D, Kramer HB, Samant RS. Solvent Precipitation SP3 (SP4) Enhances Recovery for Proteomics Sample Preparation without Magnetic Beads. Anal Chem 2022; 94:10320-10328. [PMID: 35848328 PMCID: PMC9330274 DOI: 10.1021/acs.analchem.1c04200] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Complete, reproducible extraction of protein material
is essential
for comprehensive and unbiased proteome analyses. A current gold standard
is single-pot, solid-phase-enhanced sample preparation (SP3), in which
organic solvent and magnetic beads are used to denature and capture
protein aggregates, with subsequent washes removing contaminants.
However, SP3 is dependent on effective protein immobilization onto
beads, risks losses during wash steps, and exhibits losses and greater
costs at higher protein inputs. Here, we propose solvent precipitation
SP3 (SP4) as an alternative to SP3 protein cleanup, capturing acetonitrile-induced
protein aggregates by brief centrifugation rather than magnetism—with
optional low-cost inert glass beads to simplify handling. SP4 recovered
equivalent or greater protein yields for 1–5000 μg preparations
and improved reproducibility (median protein R2 0.99 (SP4) vs 0.97 (SP3)). Deep proteome
profiling revealed that SP4 yielded a greater recovery of low-solubility
and transmembrane proteins than SP3, benefits to aggregating protein
using 80 vs 50% organic solvent, and equivalent recovery by SP4 and S-Trap.
SP4 was verified in three other labs across eight sample types and
five lysis buffers—all confirming equivalent or improved proteome
characterization vs SP3. With near-identical recovery,
this work further illustrates protein precipitation as the primary
mechanism of SP3 protein cleanup and identifies that magnetic capture
risks losses, especially at higher protein concentrations and among
more hydrophobic proteins. SP4 offers a minimalistic approach to protein
cleanup that provides cost-effective input scalability, the option
to omit beads entirely, and suggests important considerations for
SP3 applications—all while retaining the speed and compatibility
of SP3.
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Affiliation(s)
- Harvey E Johnston
- Signalling Programme, The Babraham Institute, Cambridge CB22 3AT, United Kingdom
| | - Kranthikumar Yadav
- Mass Spectrometry Facility, The Babraham Institute, Cambridge CB22 3AT, United Kingdom
| | | | - George S Biggs
- Proteomics STP, The Francis Crick Institute, London NW1 1AT, United Kingdom.,GlaxoSmithKline, Gunnels Wood Road, Stevenage SG1 2NY, Hertfordshire, United Kingdom
| | - David Oxley
- Mass Spectrometry Facility, The Babraham Institute, Cambridge CB22 3AT, United Kingdom
| | - Holger B Kramer
- Medical Research Council London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital, London W12 0NN, United Kingdom
| | - Rahul S Samant
- Signalling Programme, The Babraham Institute, Cambridge CB22 3AT, United Kingdom
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46
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Scalable multiplex co-fractionation/mass spectrometry platform for accelerated protein interactome discovery. Nat Commun 2022; 13:4043. [PMID: 35831314 PMCID: PMC9279285 DOI: 10.1038/s41467-022-31809-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 06/29/2022] [Indexed: 12/14/2022] Open
Abstract
Co-fractionation/mass spectrometry (CF/MS) enables the mapping of endogenous macromolecular networks on a proteome scale, but current methods are experimentally laborious, resource intensive and afford lesser quantitative accuracy. Here, we present a technically efficient, cost-effective and reproducible multiplex CF/MS (mCF/MS) platform for measuring and comparing, simultaneously, multi-protein assemblies across different experimental samples at a rate that is up to an order of magnitude faster than previous approaches. We apply mCF/MS to map the protein interaction landscape of non-transformed mammary epithelia versus breast cancer cells in parallel, revealing large-scale differences in protein-protein interactions and the relative abundance of associated macromolecules connected with cancer-related pathways and altered cellular processes. The integration of multiplexing capability within an optimized workflow renders mCF/MS as a powerful tool for systematically exploring physical interaction networks in a comparative manner. Co-fractionation/mass spectrometry (CF/MS) allows mapping protein interactomes but efficiency and quantitative accuracy are limited. Here, the authors develop a reproducible multiplexed CF/MS method and apply it to characterize interactome rewiring in breast cancer cells.
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Berg MD, Zhu Y, Loll-Krippleber R, San Luis BJ, Genereaux J, Boone C, Villén J, Brown GW, Brandl CJ. Genetic background and mistranslation frequency determine the impact of mistranslating tRNASerUGG. G3 GENES|GENOMES|GENETICS 2022; 12:6588684. [PMID: 35587152 PMCID: PMC9258585 DOI: 10.1093/g3journal/jkac125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 05/07/2022] [Indexed: 12/02/2022]
Abstract
Transfer RNA variants increase the frequency of mistranslation, the misincorporation of an amino acid not specified by the “standard” genetic code, to frequencies approaching 10% in yeast and bacteria. Cells cope with these variants by having multiple copies of each tRNA isodecoder and through pathways that deal with proteotoxic stress. In this study, we define the genetic interactions of the gene encoding tRNASerUGG,G26A, which mistranslates serine at proline codons. Using a collection of yeast temperature-sensitive alleles, we identify negative synthetic genetic interactions between the mistranslating tRNA and 109 alleles representing 91 genes, with nearly half of the genes having roles in RNA processing or protein folding and turnover. By regulating tRNA expression, we then compare the strength of the negative genetic interaction for a subset of identified alleles under differing amounts of mistranslation. The frequency of mistranslation correlated with the impact on cell growth for all strains analyzed; however, there were notable differences in the extent of the synthetic interaction at different frequencies of mistranslation depending on the genetic background. For many of the strains, the extent of the negative interaction with tRNASerUGG,G26A was proportional to the frequency of mistranslation or only observed at intermediate or high frequencies. For others, the synthetic interaction was approximately equivalent at all frequencies of mistranslation. As humans contain similar mistranslating tRNAs, these results are important when analyzing the impact of tRNA variants on disease, where both the individual’s genetic background and the expression of the mistranslating tRNA variant need to be considered.
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Affiliation(s)
- Matthew D Berg
- Department of Biochemistry, The University of Western Ontario , London, ON N6A 5C1, Canada
- Department of Genome Sciences, University of Washington , Seattle, WA 98195, USA
| | - Yanrui Zhu
- Department of Biochemistry, The University of Western Ontario , London, ON N6A 5C1, Canada
| | - Raphaël Loll-Krippleber
- Department of Biochemistry, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto , Toronto, ON M5S 3E1, Canada
| | - Bryan-Joseph San Luis
- Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto , Toronto, ON M5S 1A8, Canada
| | - Julie Genereaux
- Department of Biochemistry, The University of Western Ontario , London, ON N6A 5C1, Canada
| | - Charles Boone
- Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto , Toronto, ON M5S 1A8, Canada
| | - Judit Villén
- Department of Genome Sciences, University of Washington , Seattle, WA 98195, USA
| | - Grant W Brown
- Department of Biochemistry, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto , Toronto, ON M5S 3E1, Canada
| | - Christopher J Brandl
- Department of Biochemistry, The University of Western Ontario , London, ON N6A 5C1, Canada
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48
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Koenig C, Martinez-Val A, Franciosa G, Olsen JV. Optimal analytical strategies for sensitive and quantitative phosphoproteomics using TMT-based multiplexing. Proteomics 2022; 22:e2100245. [PMID: 35713889 DOI: 10.1002/pmic.202100245] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 04/28/2022] [Accepted: 06/01/2022] [Indexed: 11/10/2022]
Abstract
In large-scale quantitative mass spectrometry (MS)-based phosphoproteomics, isobaric labeling with tandem mass tags (TMTs) coupled with offline high-pH reversed-phase peptide chromatographic fractionation maximizes depth of coverage. To investigate to what extent limited sample amounts affect sensitivity and dynamic range of the analysis due to sample losses, we benchmarked TMT-based fractionation strategies against single-shot label-free quantification with spectral library-free data independent acquisition (LFQ-DIA), for different peptide input per sample. To systematically examine how peptide input amounts influence TMT-fractionation approaches in a phosphoproteomics workflow, we compared two different high-pH reversed-phase fractionation strategies, microflow (MF) and stage-tip fractionation (STF), while scaling the peptide input amount down from 12.5 to 1 μg per sample. Our results indicate that, for input amounts higher than 5 μg per sample, TMT labeling, followed by microflow fractionation (MF) and phospho-enrichment, achieves the deepest phosphoproteome coverage, even compared to single shot direct-DIA analysis. Conversely, STF of enriched phosphopeptides (STF) is optimal for lower amounts, below 5 μg/peptide per sample. As a result, we provide a decision tree to help phosphoproteomics users to choose the best workflow as a function of sample amount.
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Affiliation(s)
- Claire Koenig
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Ana Martinez-Val
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Giulia Franciosa
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Jesper V Olsen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
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49
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Heil LR, Fondrie WE, McGann CD, Federation AJ, Noble WS, MacCoss MJ, Keich U. Building Spectral Libraries from Narrow-Window Data-Independent Acquisition Mass Spectrometry Data. J Proteome Res 2022; 21:1382-1391. [PMID: 35549345 DOI: 10.1021/acs.jproteome.1c00895] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Advances in library-based methods for peptide detection from data-independent acquisition (DIA) mass spectrometry have made it possible to detect and quantify tens of thousands of peptides in a single mass spectrometry run. However, many of these methods rely on a comprehensive, high-quality spectral library containing information about the expected retention time and fragmentation patterns of peptides in the sample. Empirical spectral libraries are often generated through data-dependent acquisition and may suffer from biases as a result. Spectral libraries can be generated in silico, but these models are not trained to handle all possible post-translational modifications. Here, we propose a false discovery rate-controlled spectrum-centric search workflow to generate spectral libraries directly from gas-phase fractionated DIA tandem mass spectrometry data. We demonstrate that this strategy is able to detect phosphorylated peptides and can be used to generate a spectral library for accurate peptide detection and quantitation in wide-window DIA data. We compare the results of this search workflow to other library-free approaches and demonstrate that our search is competitive in terms of accuracy and sensitivity. These results demonstrate that the proposed workflow has the capacity to generate spectral libraries while avoiding the limitations of other methods.
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Affiliation(s)
- Lilian R Heil
- Department of Genome Sciences, University of Washington, Seattle, Washington 98105, United States
| | - William E Fondrie
- Department of Genome Sciences, University of Washington, Seattle, Washington 98105, United States
| | - Christopher D McGann
- Department of Genome Sciences, University of Washington, Seattle, Washington 98105, United States
| | - Alexander J Federation
- Department of Genome Sciences, University of Washington, Seattle, Washington 98105, United States
| | - William S Noble
- Department of Genome Sciences, University of Washington, Seattle, Washington 98105, United States.,Paul G. Allen School for Computer Science and Engineering, University of Washington, Seattle, Washington 98105, United States
| | - Michael J MacCoss
- Department of Genome Sciences, University of Washington, Seattle, Washington 98105, United States
| | - Uri Keich
- School of Mathematics and Statistics, University of Sydney, Sydney, NSW 2006, Australia
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50
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Isaacson JR, Berg MD, Charles B, Jagiello J, Villén J, Brandl CJ, Moehring AJ. A novel mistranslating tRNA model in Drosophila melanogaster has diverse, sexually dimorphic effects. G3 GENES|GENOMES|GENETICS 2022; 12:6526391. [PMID: 35143655 PMCID: PMC9073681 DOI: 10.1093/g3journal/jkac035] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 02/03/2022] [Indexed: 11/17/2022]
Abstract
Transfer RNAs (tRNAs) are the adaptor molecules required for reading the genetic code and producing proteins. Transfer RNA variants can lead to genome-wide mistranslation, the misincorporation of amino acids not specified by the standard genetic code into nascent proteins. While genome sequencing has identified putative mistranslating transfer RNA variants in human populations, little is known regarding how mistranslation affects multicellular organisms. Here, we create a multicellular model of mistranslation by integrating a serine transfer RNA variant that mistranslates serine for proline (tRNAUGG,G26ASer) into the Drosophila melanogaster genome. We confirm mistranslation via mass spectrometry and find that tRNAUGG,G26ASer misincorporates serine for proline at a frequency of ∼0.6% per codon. tRNAUGG,G26ASer extends development time and decreases the number of flies that reach adulthood. While both sexes of adult flies containing tRNAUGG,G26ASer present with morphological deformities and poor climbing performance, these effects are more pronounced in female flies and the impact on climbing performance is exacerbated by age. This model will enable studies into the synergistic effects of mistranslating transfer RNA variants and disease-causing alleles.
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Affiliation(s)
- Joshua R Isaacson
- Department of Biology, The University of Western Ontario, London, ON N6A 5B7, Canada
| | - Matthew D Berg
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5B7, Canada
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Brendan Charles
- Department of Biology, The University of Western Ontario, London, ON N6A 5B7, Canada
| | - Jessica Jagiello
- Department of Biology, The University of Western Ontario, London, ON N6A 5B7, Canada
| | - Judit Villén
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Christopher J Brandl
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5B7, Canada
| | - Amanda J Moehring
- Department of Biology, The University of Western Ontario, London, ON N6A 5B7, Canada
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