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Emery-Corbin SJ, Yousef JM, Adhikari S, Sumardy F, Nhu D, van Delft MF, Lessene G, Dziekan J, Webb AI, Dagley LF. Improved drug target deconvolution with PISA-DIA using an extended, overlapping temperature gradient. Proteomics 2024; 24:e2300644. [PMID: 38766901 DOI: 10.1002/pmic.202300644] [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: 12/19/2023] [Revised: 05/03/2024] [Accepted: 05/07/2024] [Indexed: 05/22/2024]
Abstract
Thermal proteome profiling (TPP) is a powerful tool for drug target deconvolution. Recently, data-independent acquisition mass spectrometry (DIA-MS) approaches have demonstrated significant improvements to depth and missingness in proteome data, but traditional TPP (a.k.a. CEllular Thermal Shift Assay "CETSA") workflows typically employ multiplexing reagents reliant on data-dependent acquisition (DDA). Herein, we introduce a new experimental design for the Proteome Integral Solubility Alteration via label-free DIA approach (PISA-DIA). We highlight the proteome coverage and sensitivity achieved by using multiple overlapping thermal gradients alongside DIA-MS, which maximizes efficiencies in PISA sample concatenation and safeguards against missing protein targets that exist at high melting temperatures. We demonstrate our extended PISA-DIA design has superior proteome coverage as compared to using tandem-mass tags (TMT) necessitating DDA-MS analysis. Importantly, we demonstrate our PISA-DIA approach has the quantitative and statistical rigor using A-1331852, a specific inhibitor of BCL-xL. Due to the high melt temperature of this protein target, we utilized our extended multiple gradient PISA-DIA workflow to identify BCL-xL. We assert our novel overlapping gradient PISA-DIA-MS approach is ideal for unbiased drug target deconvolution, spanning a large temperature range whilst minimizing target dropout between gradients, increasing the likelihood of resolving the protein targets of novel compounds.
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Affiliation(s)
- Samantha J Emery-Corbin
- Advanced Technology and Biology Division, the Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - Jumana M Yousef
- Advanced Technology and Biology Division, the Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - Subash Adhikari
- Advanced Technology and Biology Division, the Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - Fransisca Sumardy
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
- ACRF Chemical Biology Division, the Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
| | - Duong Nhu
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
- ACRF Chemical Biology Division, the Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
| | - Mark F van Delft
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
- Blood Cells and Blood Cancer Division, the Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
| | - Guillaume Lessene
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
- ACRF Chemical Biology Division, the Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Department of Pharmacology and Therapeutics, University of Melbourne, Melbourne, Victoria, Australia
| | - Jerzy Dziekan
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
- Infection and Immunity Division, the Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
| | - Andrew I Webb
- Advanced Technology and Biology Division, the Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - Laura F Dagley
- Advanced Technology and Biology Division, the Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
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2
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Jokumsen KV, Huhle VH, Hägglund PM, Davies MJ, Gamon LF. Elevated levels of iodide promote peroxidase-mediated protein iodination and inhibit protein chlorination. Free Radic Biol Med 2024; 220:207-221. [PMID: 38663830 DOI: 10.1016/j.freeradbiomed.2024.04.230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 04/18/2024] [Indexed: 05/15/2024]
Abstract
At inflammatory sites, immune cells generate oxidants including H₂O₂. Myeloperoxidase (MPO), released by activated leukocytes employs H₂O₂ and halide/pseudohalides to form hypohalous acids that mediate pathogen killing. Hypochlorous acid (HOCl) is a major species formed. Excessive or misplaced HOCl formation damages host tissues with this linked to multiple inflammatory diseases. Previously (Redox Biology, 2020, 28, 101331) we reported that iodide (I⁻) modulates MPO-mediated protein damage by decreasing HOCl generation with concomitant hypoiodous acid (HOI) formation. HOI may however impact on protein structure, so in this study we examined whether and how HOI, from peroxidase/H₂O₂/I⁻ systems ± Cl⁻, modifies proteins. Experiments employed MPO and lactoperoxidase (LPO) and multiple proteins (serum albumins, anastellin), with both chemical (intact protein and peptide mass mapping, LC-MS) and structural (SDS-PAGE) changes assessed. LC-MS analyses revealed dose-dependent iodination of anastellin and albumins by LPO/H2O2 with increasing I⁻. Incubation of BSA with MPO/H2O2/Cl⁻ revealed modest chlorination (Tyr286, Tyr475, ∼4 %) and Met modification. Lower levels of these species, and extensive iodination at specific Tyr and His residues (>20 % modification with ≥10 μM I⁻) were detected with increasing I⁻. Anastellin dimerization was inhibited by increasing I⁻, but less marked changes were observed with albumins. These data confirm that I⁻ competes with Cl⁻ for MPO and is an efficient HOCl scavenger. These processes decrease protein chlorination and oxidation, but result in extensive iodination. This is consistent with published data on the presence of iodinated Tyr on neutrophil proteins. The biological implications of protein iodination relative to chlorination require further clarification.
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Affiliation(s)
| | - Valerie H Huhle
- Dept. of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark; Department of Neuropathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
| | - Per M Hägglund
- Dept. of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Michael J Davies
- Dept. of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Luke F Gamon
- Dept. of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark.
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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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Fietz D, Sgaier R, O’Donnell L, Stanton PG, Dagley LF, Webb AI, Schuppe HC, Diemer T, Pilatz A. Proteomic biomarkers in seminal plasma as predictors of reproductive potential in azoospermic men. Front Endocrinol (Lausanne) 2024; 15:1327800. [PMID: 38654926 PMCID: PMC11035875 DOI: 10.3389/fendo.2024.1327800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 03/20/2024] [Indexed: 04/26/2024] Open
Abstract
Introduction Azoospermia, characterized by an absence of sperm in the ejaculate, represents the most severe form of male infertility. While surgical sperm retrieval in obstructive azoospermia (OA) is successful in the majority of cases, patients with non-obstructive azoospermia (NOA) show retrieval rates of only about 50% and thus frequently have unnecessary surgery. Surgical intervention could be avoided if patients without preserved spermatogenesis are identified preoperatively. This prospective study aimed to discover biomarkers in seminal plasma that could be employed for a non-invasive differential diagnosis of OA/NOA in order to rationalize surgery recommendations and improve success rates. Methods All patients signed written informed consent, underwent comprehensive andrological evaluation, received human genetics to exclude relevant pathologies, and patients with azoospermia underwent surgical sperm retrieval. Using label-free LC-MS/MS, we compared the proteomes of seminal plasma samples from fertile men (healthy controls (HC), n=8) and infertile men diagnosed with 1) OA (n=7), 2) NOA with successful sperm retrieval (mixed testicular atrophy (MTA), n=8), and 3) NOA without sperm retrieval (Sertoli cell-only phenotype (SCO), n=7). Relative abundance changes of two candidate markers of sperm retrieval, HSPA2 and LDHC, were confirmed by Western Blot. Results We found the protein expression levels of 42 proteins to be significantly down-regulated (p ≤ 0.05) in seminal plasma from SCO NOA patients relative to HC whereas only one protein was down-regulated in seminal plasma from MTA patients. Analysis of tissue and cell expression suggested that the testis-specific proteins LDHC, PGK2, DPEP3, and germ-cell enriched heat-shock proteins HSPA2 and HSPA4L are promising biomarkers of spermatogenic function. Western blotting revealed a significantly lower abundance of LDHC and HSPA2 in the seminal plasma of men with NOA (SCO and MTA) compared to controls. Discussion The results indicate that certain testis-specific proteins when measured in seminal plasma, could serve as indicators of the presence of sperm in the testis and predict the success of sperm retrieval. Used in conjunction with conventional clinical assessments, these proteomic biomarkers may assist in the non-invasive diagnosis of idiopathic male infertility.
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Affiliation(s)
- Daniela Fietz
- Department of Veterinary Anatomy, Histology and Embryology, Justus Liebig University Giessen, Giessen, Germany
| | - Raouda Sgaier
- Department of Veterinary Anatomy, Histology and Embryology, Justus Liebig University Giessen, Giessen, Germany
- Centre for Reproductive Health, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Urology, Pediatric Urology and Andrology, Justus Liebig University Giessen, Giessen, Germany
| | - Liza O’Donnell
- Centre for Reproductive Health, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Molecular and Translational Sciences, Monash University, Clayton, VIC, Australia
| | - Peter G. Stanton
- Centre for Reproductive Health, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Molecular and Translational Sciences, Monash University, Clayton, VIC, Australia
| | - Laura F. Dagley
- Advanced Technology and Biology Division, Walter and Eliza Hall Institute, Parkville, VIC, Australia
- Department of Molecular and Translational Sciences, School of Clinical Sciences, Monash University, Clayton, VIC, Australia
| | - Andrew I. Webb
- Advanced Technology and Biology Division, Walter and Eliza Hall Institute, Parkville, VIC, Australia
- Department of Molecular and Translational Sciences, School of Clinical Sciences, Monash University, Clayton, VIC, Australia
| | - Hans-Christian Schuppe
- Department of Urology, Pediatric Urology and Andrology, Justus Liebig University Giessen, Giessen, Germany
| | - Thorsten Diemer
- Department of Urology, Pediatric Urology and Andrology, Justus Liebig University Giessen, Giessen, Germany
| | - Adrian Pilatz
- Department of Urology, Pediatric Urology and Andrology, Justus Liebig University Giessen, Giessen, Germany
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Lee CY, The M, Meng C, Bayer FP, Putzker K, Müller J, Streubel J, Woortman J, Sakhteman A, Resch M, Schneider A, Wilhelm S, Kuster B. Illuminating phenotypic drug responses of sarcoma cells to kinase inhibitors by phosphoproteomics. Mol Syst Biol 2024; 20:28-55. [PMID: 38177929 PMCID: PMC10883282 DOI: 10.1038/s44320-023-00004-7] [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: 12/23/2022] [Revised: 11/06/2023] [Accepted: 11/30/2023] [Indexed: 01/06/2024] Open
Abstract
Kinase inhibitors (KIs) are important cancer drugs but often feature polypharmacology that is molecularly not understood. This disconnect is particularly apparent in cancer entities such as sarcomas for which the oncogenic drivers are often not clear. To investigate more systematically how the cellular proteotypes of sarcoma cells shape their response to molecularly targeted drugs, we profiled the proteomes and phosphoproteomes of 17 sarcoma cell lines and screened the same against 150 cancer drugs. The resulting 2550 phenotypic profiles revealed distinct drug responses and the cellular activity landscapes derived from deep (phospho)proteomes (9-10,000 proteins and 10-27,000 phosphorylation sites per cell line) enabled several lines of analysis. For instance, connecting the (phospho)proteomic data with drug responses revealed known and novel mechanisms of action (MoAs) of KIs and identified markers of drug sensitivity or resistance. All data is publicly accessible via an interactive web application that enables exploration of this rich molecular resource for a better understanding of active signalling pathways in sarcoma cells, identifying treatment response predictors and revealing novel MoA of clinical KIs.
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Affiliation(s)
- Chien-Yun Lee
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Matthew The
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Chen Meng
- Bavarian Biomolecular Mass Spectrometry Center (BayBioMS), Technical University of Munich, Freising, Germany
| | - Florian P Bayer
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Kerstin Putzker
- Chemical Biology Core Facility, EMBL Heidelberg, Heidelberg, Germany
| | - Julian Müller
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Johanna Streubel
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Julia Woortman
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Amirhossein Sakhteman
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Moritz Resch
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Annika Schneider
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Stephanie Wilhelm
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, 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.
- German Cancer Consortium (DKTK), partner site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany.
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Pade LR, Stepler KE, Portero EP, DeLaney K, Nemes P. Biological mass spectrometry enables spatiotemporal 'omics: From tissues to cells to organelles. MASS SPECTROMETRY REVIEWS 2024; 43:106-138. [PMID: 36647247 PMCID: PMC10668589 DOI: 10.1002/mas.21824] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/14/2022] [Accepted: 09/17/2022] [Indexed: 06/17/2023]
Abstract
Biological processes unfold across broad spatial and temporal dimensions, and measurement of the underlying molecular world is essential to their understanding. Interdisciplinary efforts advanced mass spectrometry (MS) into a tour de force for assessing virtually all levels of the molecular architecture, some in exquisite detection sensitivity and scalability in space-time. In this review, we offer vignettes of milestones in technology innovations that ushered sample collection and processing, chemical separation, ionization, and 'omics analyses to progressively finer resolutions in the realms of tissue biopsies and limited cell populations, single cells, and subcellular organelles. Also highlighted are methodologies that empowered the acquisition and analysis of multidimensional MS data sets to reveal proteomes, peptidomes, and metabolomes in ever-deepening coverage in these limited and dynamic specimens. In pursuit of richer knowledge of biological processes, we discuss efforts pioneering the integration of orthogonal approaches from molecular and functional studies, both within and beyond MS. With established and emerging community-wide efforts ensuring scientific rigor and reproducibility, spatiotemporal MS emerged as an exciting and powerful resource to study biological systems in space-time.
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Affiliation(s)
- Leena R. Pade
- Department of Chemistry & Biochemistry, University of Maryland, 8051 Regents Drive, College Park, MD 20742
| | - Kaitlyn E. Stepler
- Department of Chemistry & Biochemistry, University of Maryland, 8051 Regents Drive, College Park, MD 20742
| | - Erika P. Portero
- Department of Chemistry & Biochemistry, University of Maryland, 8051 Regents Drive, College Park, MD 20742
| | - Kellen DeLaney
- Department of Chemistry & Biochemistry, University of Maryland, 8051 Regents Drive, College Park, MD 20742
| | - Peter Nemes
- Department of Chemistry & Biochemistry, University of Maryland, 8051 Regents Drive, College Park, MD 20742
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7
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Dowling P, Swandulla D, Ohlendieck K. Mass Spectrometry-Based Proteomic Technology and Its Application to Study Skeletal Muscle Cell Biology. Cells 2023; 12:2560. [PMID: 37947638 PMCID: PMC10649384 DOI: 10.3390/cells12212560] [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: 10/06/2023] [Revised: 10/27/2023] [Accepted: 10/31/2023] [Indexed: 11/12/2023] Open
Abstract
Voluntary striated muscles are characterized by a highly complex and dynamic proteome that efficiently adapts to changed physiological demands or alters considerably during pathophysiological dysfunction. The skeletal muscle proteome has been extensively studied in relation to myogenesis, fiber type specification, muscle transitions, the effects of physical exercise, disuse atrophy, neuromuscular disorders, muscle co-morbidities and sarcopenia of old age. Since muscle tissue accounts for approximately 40% of body mass in humans, alterations in the skeletal muscle proteome have considerable influence on whole-body physiology. This review outlines the main bioanalytical avenues taken in the proteomic characterization of skeletal muscle tissues, including top-down proteomics focusing on the characterization of intact proteoforms and their post-translational modifications, bottom-up proteomics, which is a peptide-centric method concerned with the large-scale detection of proteins in complex mixtures, and subproteomics that examines the protein composition of distinct subcellular fractions. Mass spectrometric studies over the last two decades have decisively improved our general cell biological understanding of protein diversity and the heterogeneous composition of individual myofibers in skeletal muscles. This detailed proteomic knowledge can now be integrated with findings from other omics-type methodologies to establish a systems biological view of skeletal muscle function.
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Affiliation(s)
- Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland;
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, W23 F2H6 Maynooth, Co. Kildare, Ireland
| | - Dieter Swandulla
- Institute of Physiology, Faculty of Medicine, University of Bonn, D53115 Bonn, Germany;
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland;
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, W23 F2H6 Maynooth, Co. Kildare, Ireland
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Dowling P, Gargan S, Zweyer M, Swandulla D, Ohlendieck K. Extracellular Matrix Proteomics: The mdx-4cv Mouse Diaphragm as a Surrogate for Studying Myofibrosis in Dystrophinopathy. Biomolecules 2023; 13:1108. [PMID: 37509144 PMCID: PMC10377647 DOI: 10.3390/biom13071108] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 07/06/2023] [Accepted: 07/10/2023] [Indexed: 07/30/2023] Open
Abstract
The progressive degeneration of the skeletal musculature in Duchenne muscular dystrophy is accompanied by reactive myofibrosis, fat substitution, and chronic inflammation. Fibrotic changes and reduced tissue elasticity correlate with the loss in motor function in this X-chromosomal disorder. Thus, although dystrophinopathies are due to primary abnormalities in the DMD gene causing the almost-complete absence of the cytoskeletal Dp427-M isoform of dystrophin in voluntary muscles, the excessive accumulation of extracellular matrix proteins presents a key histopathological hallmark of muscular dystrophy. Animal model research has been instrumental in the characterization of dystrophic muscles and has contributed to a better understanding of the complex pathogenesis of dystrophinopathies, the discovery of new disease biomarkers, and the testing of novel therapeutic strategies. In this article, we review how mass-spectrometry-based proteomics can be used to study changes in key components of the endomysium, perimysium, and epimysium, such as collagens, proteoglycans, matricellular proteins, and adhesion receptors. The mdx-4cv mouse diaphragm displays severe myofibrosis, making it an ideal model system for large-scale surveys of systematic alterations in the matrisome of dystrophic fibers. Novel biomarkers of myofibrosis can now be tested for their appropriateness in the preclinical and clinical setting as diagnostic, pharmacodynamic, prognostic, and/or therapeutic monitoring indicators.
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Affiliation(s)
- Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland
| | - Stephen Gargan
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland
| | - Margit Zweyer
- Department of Neonatology and Paediatric Intensive Care, Children's Hospital, German Center for Neurodegenerative Diseases, University of Bonn, D53127 Bonn, Germany
| | - Dieter Swandulla
- Institute of Physiology, Medical Faculty, University of Bonn, D53115 Bonn, Germany
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland
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Ryan FJ, Norton TS, McCafferty C, Blake SJ, Stevens NE, James J, Eden GL, Tee YC, Benson SC, Masavuli MG, Yeow AEL, Abayasingam A, Agapiou D, Stevens H, Zecha J, Messina NL, Curtis N, Ignjatovic V, Monagle P, Tran H, McFadyen JD, Bull RA, Grubor-Bauk B, Lynn MA, Botten R, Barry SE, Lynn DJ. A systems immunology study comparing innate and adaptive immune responses in adults to COVID-19 mRNA and adenovirus vectored vaccines. Cell Rep Med 2023; 4:100971. [PMID: 36871558 PMCID: PMC9935276 DOI: 10.1016/j.xcrm.2023.100971] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 12/23/2022] [Accepted: 02/13/2023] [Indexed: 02/19/2023]
Abstract
Identifying the molecular mechanisms that promote optimal immune responses to coronavirus disease 2019 (COVID-19) vaccination is critical for future rational vaccine design. Here, we longitudinally profile innate and adaptive immune responses in 102 adults after the first, second, and third doses of mRNA or adenovirus-vectored COVID-19 vaccines. Using a multi-omics approach, we identify key differences in the immune responses induced by ChAdOx1-S and BNT162b2 that correlate with antigen-specific antibody and T cell responses or vaccine reactogenicity. Unexpectedly, we observe that vaccination with ChAdOx1-S, but not BNT162b2, induces an adenoviral vector-specific memory response after the first dose, which correlates with the expression of proteins with roles in thrombosis with potential implications for thrombosis with thrombocytopenia syndrome (TTS), a rare but serious adverse event linked to adenovirus-vectored vaccines. The COVID-19 Vaccine Immune Responses Study thus represents a major resource that can be used to understand the immunogenicity and reactogenicity of these COVID-19 vaccines.
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Affiliation(s)
- Feargal J Ryan
- Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, SA 5001, Australia; Flinders Health and Medical Research Institute, Flinders University, Bedford Park, SA 5042, Australia
| | - Todd S Norton
- Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, SA 5001, Australia
| | - Conor McCafferty
- Haematology Research, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia; Department of Paediatrics, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Stephen J Blake
- Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, SA 5001, Australia; Flinders Health and Medical Research Institute, Flinders University, Bedford Park, SA 5042, Australia
| | - Natalie E Stevens
- Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, SA 5001, Australia; Flinders Health and Medical Research Institute, Flinders University, Bedford Park, SA 5042, Australia
| | - Jane James
- Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, SA 5001, Australia
| | - Georgina L Eden
- Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, SA 5001, Australia
| | - Yee C Tee
- Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, SA 5001, Australia; Flinders Health and Medical Research Institute, Flinders University, Bedford Park, SA 5042, Australia
| | - Saoirse C Benson
- Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, SA 5001, Australia; Flinders Health and Medical Research Institute, Flinders University, Bedford Park, SA 5042, Australia
| | - Makutiro G Masavuli
- Viral Immunology Group, Adelaide Medical School, University of Adelaide and Basil Hetzel Institute for Translational Health Research, Adelaide, SA 5011, Australia
| | - Arthur E L Yeow
- Viral Immunology Group, Adelaide Medical School, University of Adelaide and Basil Hetzel Institute for Translational Health Research, Adelaide, SA 5011, Australia
| | - Arunasingam Abayasingam
- School of Medical Sciences, Faculty of Medicine, UNSW, Sydney, NSW 2052, Australia; The Kirby Institute, Sydney, NSW 2052, Australia
| | | | - Hannah Stevens
- Clinical Haematology Department, Alfred Hospital, Melbourne, VIC 3004, Australia; Australian Centre for Blood Diseases, Monash University, Melbourne, VIC 3800, Australia
| | - Jana Zecha
- Dynamic Omics, Centre for Genomics Research, Discovery Sciences, R&D, AstraZeneca, Gaithersburg, MD 20878, USA
| | - Nicole L Messina
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3010, Australia; Infectious Diseases Group, Murdoch Children's Research Institute, Parkville, VIC 3052, Australia
| | - Nigel Curtis
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3010, Australia; Infectious Diseases Group, Murdoch Children's Research Institute, Parkville, VIC 3052, Australia
| | - Vera Ignjatovic
- Haematology Research, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia; Department of Paediatrics, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Paul Monagle
- Haematology Research, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia; Department of Paediatrics, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Huyen Tran
- Clinical Haematology Department, Alfred Hospital, Melbourne, VIC 3004, Australia; Australian Centre for Blood Diseases, Monash University, Melbourne, VIC 3800, Australia
| | - James D McFadyen
- Clinical Haematology Department, Alfred Hospital, Melbourne, VIC 3004, Australia; Atherothrombosis and Vascular Biology Program, Baker Heart and Diabetes Institute, Melbourne, VIC 3004, Australia; Baker Department of Cardiometabolic Health, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Rowena A Bull
- School of Medical Sciences, Faculty of Medicine, UNSW, Sydney, NSW 2052, Australia; The Kirby Institute, Sydney, NSW 2052, Australia
| | - Branka Grubor-Bauk
- Viral Immunology Group, Adelaide Medical School, University of Adelaide and Basil Hetzel Institute for Translational Health Research, Adelaide, SA 5011, Australia
| | - Miriam A Lynn
- Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, SA 5001, Australia; Flinders Health and Medical Research Institute, Flinders University, Bedford Park, SA 5042, Australia
| | - Rochelle Botten
- Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, SA 5001, Australia
| | - Simone E Barry
- Department of Thoracic Medicine, Royal Adelaide Hospital, Adelaide, SA 5000, Australia
| | - David J Lynn
- Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, SA 5001, Australia; Flinders Health and Medical Research Institute, Flinders University, Bedford Park, SA 5042, Australia.
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10
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Bottom-Up Proteomics: Advancements in Sample Preparation. Int J Mol Sci 2023; 24:ijms24065350. [PMID: 36982423 PMCID: PMC10049050 DOI: 10.3390/ijms24065350] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 02/28/2023] [Accepted: 03/09/2023] [Indexed: 03/14/2023] Open
Abstract
Liquid chromatography–tandem mass spectrometry (LC–MS/MS)-based proteomics is a powerful technique for profiling proteomes of cells, tissues, and body fluids. Typical bottom-up proteomic workflows consist of the following three major steps: sample preparation, LC–MS/MS analysis, and data analysis. LC–MS/MS and data analysis techniques have been intensively developed, whereas sample preparation, a laborious process, remains a difficult task and the main challenge in different applications. Sample preparation is a crucial stage that affects the overall efficiency of a proteomic study; however, it is prone to errors and has low reproducibility and throughput. In-solution digestion and filter-aided sample preparation are the typical and widely used methods. In the past decade, novel methods to improve and facilitate the entire sample preparation process or integrate sample preparation and fractionation have been reported to reduce time, increase throughput, and improve reproducibility. In this review, we have outlined the current methods used for sample preparation in proteomics, including on-membrane digestion, bead-based digestion, immobilized enzymatic digestion, and suspension trapping. Additionally, we have summarized and discussed current devices and methods for integrating different steps of sample preparation and peptide fractionation.
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11
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Nickerson JL, Baghalabadi V, Rajendran SRCK, Jakubec PJ, Said H, McMillen TS, Dang Z, Doucette AA. Recent advances in top-down proteome sample processing ahead of MS analysis. MASS SPECTROMETRY REVIEWS 2023; 42:457-495. [PMID: 34047392 DOI: 10.1002/mas.21706] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 04/21/2021] [Accepted: 05/06/2021] [Indexed: 06/12/2023]
Abstract
Top-down proteomics is emerging as a preferred approach to investigate biological systems, with objectives ranging from the detailed assessment of a single protein therapeutic, to the complete characterization of every possible protein including their modifications, which define the human proteoform. Given the controlling influence of protein modifications on their biological function, understanding how gene products manifest or respond to disease is most precisely achieved by characterization at the intact protein level. Top-down mass spectrometry (MS) analysis of proteins entails unique challenges associated with processing whole proteins while maintaining their integrity throughout the processes of extraction, enrichment, purification, and fractionation. Recent advances in each of these critical front-end preparation processes, including minimalistic workflows, have greatly expanded the capacity of MS for top-down proteome analysis. Acknowledging the many contributions in MS technology and sample processing, the present review aims to highlight the diverse strategies that have forged a pathway for top-down proteomics. We comprehensively discuss the evolution of front-end workflows that today facilitate optimal characterization of proteoform-driven biology, including a brief description of the clinical applications that have motivated these impactful contributions.
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Affiliation(s)
| | - Venus Baghalabadi
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Subin R C K Rajendran
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
- Verschuren Centre for Sustainability in Energy and the Environment, Sydney, Nova Scotia, Canada
| | - Philip J Jakubec
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Hammam Said
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Teresa S McMillen
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Ziheng Dang
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Alan A Doucette
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
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12
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Dowling P, Gargan S, Swandulla D, Ohlendieck K. Fiber-Type Shifting in Sarcopenia of Old Age: Proteomic Profiling of the Contractile Apparatus of Skeletal Muscles. Int J Mol Sci 2023; 24:2415. [PMID: 36768735 PMCID: PMC9916839 DOI: 10.3390/ijms24032415] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/20/2023] [Accepted: 01/23/2023] [Indexed: 01/28/2023] Open
Abstract
The progressive loss of skeletal muscle mass and concomitant reduction in contractile strength plays a central role in frailty syndrome. Age-related neuronal impairments are closely associated with sarcopenia in the elderly, which is characterized by severe muscular atrophy that can considerably lessen the overall quality of life at old age. Mass-spectrometry-based proteomic surveys of senescent human skeletal muscles, as well as animal models of sarcopenia, have decisively improved our understanding of the molecular and cellular consequences of muscular atrophy and associated fiber-type shifting during aging. This review outlines the mass spectrometric identification of proteome-wide changes in atrophying skeletal muscles, with a focus on contractile proteins as potential markers of changes in fiber-type distribution patterns. The observed trend of fast-to-slow transitions in individual human skeletal muscles during the aging process is most likely linked to a preferential susceptibility of fast-twitching muscle fibers to muscular atrophy. Studies with senescent animal models, including mostly aged rodent skeletal muscles, have confirmed fiber-type shifting. The proteomic analysis of fast versus slow isoforms of key contractile proteins, such as myosin heavy chains, myosin light chains, actins, troponins and tropomyosins, suggests them as suitable bioanalytical tools of fiber-type transitions during aging.
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Affiliation(s)
- Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, W23 F2H6 Maynooth, Co. Kildare, Ireland
| | - Stephen Gargan
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, W23 F2H6 Maynooth, Co. Kildare, Ireland
| | - Dieter Swandulla
- Institute of Physiology, University of Bonn, D53115 Bonn, Germany
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, W23 F2H6 Maynooth, Co. Kildare, Ireland
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13
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Carrillo-Rodriguez P, Selheim F, Hernandez-Valladares M. Mass Spectrometry-Based Proteomics Workflows in Cancer Research: The Relevance of Choosing the Right Steps. Cancers (Basel) 2023; 15:555. [PMID: 36672506 PMCID: PMC9856946 DOI: 10.3390/cancers15020555] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 01/12/2023] [Indexed: 01/19/2023] Open
Abstract
The qualitative and quantitative evaluation of proteome changes that condition cancer development can be achieved with liquid chromatography-mass spectrometry (LC-MS). LC-MS-based proteomics strategies are carried out according to predesigned workflows that comprise several steps such as sample selection, sample processing including labeling, MS acquisition methods, statistical treatment, and bioinformatics to understand the biological meaning of the findings and set predictive classifiers. As the choice of best options might not be straightforward, we herein review and assess past and current proteomics approaches for the discovery of new cancer biomarkers. Moreover, we review major bioinformatics tools for interpreting and visualizing proteomics results and suggest the most popular machine learning techniques for the selection of predictive biomarkers. Finally, we consider the approximation of proteomics strategies for clinical diagnosis and prognosis by discussing current barriers and proposals to circumvent them.
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Affiliation(s)
- Paula Carrillo-Rodriguez
- Proteomics Unit of University of Bergen (PROBE), University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway
- Vall d’Hebron Institute of Oncology (VHIO), 08035 Barcelona, Spain
| | - Frode Selheim
- Proteomics Unit of University of Bergen (PROBE), University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway
| | - Maria Hernandez-Valladares
- Proteomics Unit of University of Bergen (PROBE), University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway
- Department of Physical Chemistry, University of Granada, Avenida de la Fuente Nueva S/N, 18071 Granada, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, 18012 Granada, Spain
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14
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Längrich T, Bork K, Horstkorte R, Weber V, Hofmann B, Fuszard M, Olzscha H. Disturbance of Key Cellular Subproteomes upon Propofol Treatment Is Associated with Increased Permeability of the Blood-Brain Barrier. Proteomes 2022; 10:proteomes10030028. [PMID: 35997440 PMCID: PMC9397097 DOI: 10.3390/proteomes10030028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 08/02/2022] [Accepted: 08/03/2022] [Indexed: 11/16/2022] Open
Abstract
Background: Propofol is a short-acting anesthetic, which is often used for induction and maintenance of general anesthesia, sedation for mechanically ventilated adults and procedural sedation. Several side effects of propofol are known and a substantial number of patients suffer from post-operative delirium after propofol application. In this study, we analyzed the effect of propofol on the function and protein expression profile on a proteome-wide scale. Methods: We cultured human brain microvascular endothelial cells in absence and presence of propofol and analyzed the permeability of the blood-brain barrier (BBB) by fluorescein passage and protein abundance on a proteome-wide scale by mass spectrometry. Results: Propofol interfered with the function of the blood-brain barrier. This was not due to decreased adhesion of propofol-treated human brain microvascular endothelial cells. The proteomic analysis revealed that some key pathways in these cells were disturbed, such as oxygen metabolism, DNA damage recognition and response to stress. Conclusions: Propofol has strong effects on protein expression which could explain several side effects of propofol.
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Affiliation(s)
- Timo Längrich
- Institut für Physiologische Chemie, Martin-Luther-Universität Halle-Wittenberg, Hollystr. 1, 06114 Halle (Saale), Germany
| | - Kaya Bork
- Institut für Physiologische Chemie, Martin-Luther-Universität Halle-Wittenberg, Hollystr. 1, 06114 Halle (Saale), Germany
| | - Rüdiger Horstkorte
- Institut für Physiologische Chemie, Martin-Luther-Universität Halle-Wittenberg, Hollystr. 1, 06114 Halle (Saale), Germany
| | - Veronika Weber
- Institut für Physiologische Chemie, Martin-Luther-Universität Halle-Wittenberg, Hollystr. 1, 06114 Halle (Saale), Germany
| | - Britt Hofmann
- Klinik und Poliklinik für Herzchirurgie, Universitätsklinikum Halle (Saale), Ernst-Grube-Str. 20, 06120 Halle (Saale), Germany
| | - Matt Fuszard
- Core Facility—Proteomic Mass Spectrometry, Proteinzentrum Charles Tanford, Kurt-Mothes-Straße 3a, 06120 Halle (Saale), Germany
| | - Heidi Olzscha
- Institut für Physiologische Chemie, Martin-Luther-Universität Halle-Wittenberg, Hollystr. 1, 06114 Halle (Saale), Germany
- Medical School Hamburg MSH, University of Applied Sciences and Medical University, Institute of Molecular Medicine, Am Sandtorkai 76, 20457 Hamburg, Germany
- Correspondence:
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15
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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: 25] [Impact Index Per Article: 12.5] [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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16
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Maráková K. The Crucial Step in Every Analytical Workflow: Sample Preparation—Are We Ready For a Growing Area of Intact Protein Analysis? LCGC NORTH AMERICA 2022. [DOI: 10.56530/lcgc.na.ci1888f7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Proteins are biomolecules with a lot of essential functions in a human body. Their varied expression during complex disorders, including cancer, predicts their potential use as biomarkers. Therefore, there is a need for reliable analytical workflows for their analysis in complex biological matrices. Despite the very sensitive and advanced instrumentation we have available for protein analysis today, sample preparation still remains one of the biggest challenges.
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17
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Kaulich PT, Winkels K, Kaulich TB, Treitz C, Cassidy L, Tholey A. MSTopDiff: A Tool for the Visualization of Mass Shifts in Deconvoluted Top-Down Proteomics Data for the Database-Independent Detection of Protein Modifications. J Proteome Res 2021; 21:20-29. [PMID: 34818005 DOI: 10.1021/acs.jproteome.1c00766] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Top-down proteomics analyzes intact proteoforms with all of their post-translational modifications and genetic and RNA splice variants. In addition, modifications introduced either deliberately or inadvertently during sample preparation, that is, via oxidation, alkylation, or labeling reagents, or through the formation of noncovalent adducts (e.g., detergents) further increase the sample complexity. To facilitate the recognition of protein modifications introduced during top-down analysis, we developed MSTopDiff, a software tool with a graphical user interface written in Python, which allows one to detect protein modifications by calculating and visualizing mass differences in top-down data without the prerequisite of a database search. We demonstrate the successful application of MSTopDiff for the detection of artifacts originating from oxidation, formylation, overlabeling during isobaric labeling, and adduct formation with cations or sodium dodecyl sulfate. MSTopDiff offers several modes of data representation using deconvoluted MS1 or MS2 spectra. In addition to artificial modifications, the tool enables the visualization of biological modifications such as phosphorylation and acetylation. MSTopDiff provides an overview of the artificial and biological modifications in top-down proteomics samples, which makes it a valuable tool in quality control of standard workflows and for parameter evaluation during method development.
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Affiliation(s)
- Philipp T Kaulich
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, 24105 Kiel, Germany
| | - Konrad Winkels
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, 24105 Kiel, Germany
| | - Tobias B Kaulich
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, 24105 Kiel, Germany
| | - Christian Treitz
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, 24105 Kiel, Germany
| | - Liam Cassidy
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, 24105 Kiel, Germany
| | - Andreas Tholey
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, 24105 Kiel, Germany
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18
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Kassem S, van der Pan K, de Jager AL, Naber BAE, de Laat IF, Louis A, van Dongen JJM, Teodosio C, Díez P. Proteomics for Low Cell Numbers: How to Optimize the Sample Preparation Workflow for Mass Spectrometry Analysis. J Proteome Res 2021; 20:4217-4230. [PMID: 34328739 PMCID: PMC8419858 DOI: 10.1021/acs.jproteome.1c00321] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Indexed: 12/20/2022]
Abstract
Nowadays, massive genomics and transcriptomics data can be generated at the single-cell level. However, proteomics in this setting is still a big challenge. Despite the great improvements in sensitivity and performance of mass spectrometry instruments and the better knowledge on sample preparation processing, it is widely acknowledged that multistep proteomics workflows may lead to substantial sample loss, especially when working with paucicellular samples. Still, in clinical fields, frequently limited sample amounts are available for downstream analysis, thereby hampering comprehensive characterization at protein level. To aim at better protein and peptide recoveries, we compare existing and novel approaches in the multistep sample preparation protocols for mass spectrometry studies, from sample collection, cell lysis, protein quantification, and electrophoresis/staining to protein digestion, peptide recovery, and LC-MS/MS instruments. From this critical evaluation, we conclude that the recent innovations and technologies, together with high quality management of samples, make proteomics on paucicellular samples possible, which will have immediate impact for the proteomics community.
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Affiliation(s)
- Sara Kassem
- Department
of Immunology, Leiden University Medical
Center (LUMC), Albinusdreef 2, 2333ZA Leiden, Netherlands
| | - Kyra van der Pan
- Department
of Immunology, Leiden University Medical
Center (LUMC), Albinusdreef 2, 2333ZA Leiden, Netherlands
| | - Anniek L. de Jager
- Department
of Immunology, Leiden University Medical
Center (LUMC), Albinusdreef 2, 2333ZA Leiden, Netherlands
| | - Brigitta A. E. Naber
- Department
of Immunology, Leiden University Medical
Center (LUMC), Albinusdreef 2, 2333ZA Leiden, Netherlands
| | - Inge F. de Laat
- Department
of Immunology, Leiden University Medical
Center (LUMC), Albinusdreef 2, 2333ZA Leiden, Netherlands
| | - Alesha Louis
- Department
of Immunology, Leiden University Medical
Center (LUMC), Albinusdreef 2, 2333ZA Leiden, Netherlands
| | - Jacques J. M. van Dongen
- Department
of Immunology, Leiden University Medical
Center (LUMC), Albinusdreef 2, 2333ZA Leiden, Netherlands
| | - Cristina Teodosio
- Department
of Immunology, Leiden University Medical
Center (LUMC), Albinusdreef 2, 2333ZA Leiden, Netherlands
| | - Paula Díez
- Department
of Immunology, Leiden University Medical
Center (LUMC), Albinusdreef 2, 2333ZA Leiden, Netherlands
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19
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Grbac E, So T, Varshney S, Williamson N, Dimitriadis E, Menkhorst E. Prednisolone Alters Endometrial Decidual Cells and Affects Decidual-Trophoblast Interactions. Front Cell Dev Biol 2021; 9:647496. [PMID: 33898438 PMCID: PMC8063028 DOI: 10.3389/fcell.2021.647496] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 03/18/2021] [Indexed: 12/14/2022] Open
Abstract
Poor pregnancy outcomes such as recurrent pregnancy loss (RPL) and preeclampsia are associated with impaired decidualization and abnormal trophoblast invasion. Emerging evidence suggests that use of corticosteroids, including prednisolone affects fertility by altering uterine function and may be associated with preeclampsia incidence. In this study, using primary and gestational-age appropriate tissue, we aimed to define the effect of prednisolone on human endometrial stromal fibroblast (hESF) decidualization and determine whether hESF decidualization in the presence of prednisolone would alter hESF regulation of trophoblast function. We found that prednisolone treatment reduced hESF cytokine expression (IL6, IL11, IL18, LIF, and LIFR) but had no effect on hESF expression or secretion of the classic markers of decidualization [prolactin (PRL) and IGFBP1]. Using proteomics we determined that prednisolone altered decidualized hESF protein production, enriching hESF proteins associated with acetylation and mitrochondria. Conditioned media from hESF decidualized in the presence of prednisolone significantly enhanced trophoblast outgrowth and trophoblast mRNA expression of cell motility gene PLCG1 and reduced trophoblast production of PGF. Prednisolone treatment during the menstrual cycle and 1st trimester of pregnancy might alter decidual interactions with other cells, including invasive trophoblast.
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Affiliation(s)
- Eliza Grbac
- Department of Obstetrics and Gynaecology, The University of Melbourne, Parkville, VIC, Australia.,Gynaecology Research Centre, Royal Women's Hospital, Parkville, VIC, Australia
| | - Teresa So
- Department of Obstetrics and Gynaecology, The University of Melbourne, Parkville, VIC, Australia.,Gynaecology Research Centre, Royal Women's Hospital, Parkville, VIC, Australia
| | - Swati Varshney
- Melbourne Mass Spectrometry and Proteomics Facility, Bio21 Molecular Science and Biotechnology, Parkville, VIC, Australia
| | - Nicholas Williamson
- Melbourne Mass Spectrometry and Proteomics Facility, Bio21 Molecular Science and Biotechnology, Parkville, VIC, Australia
| | - Evdokia Dimitriadis
- Department of Obstetrics and Gynaecology, The University of Melbourne, Parkville, VIC, Australia.,Gynaecology Research Centre, Royal Women's Hospital, Parkville, VIC, Australia.,Centre for Reproductive Health, Hudson Institute of Medical Research, Clayton, VIC, Australia.,Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia
| | - Ellen Menkhorst
- Department of Obstetrics and Gynaecology, The University of Melbourne, Parkville, VIC, Australia.,Gynaecology Research Centre, Royal Women's Hospital, Parkville, VIC, Australia
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20
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Mikulášek K, Konečná H, Potěšil D, Holánková R, Havliš J, Zdráhal Z. SP3 Protocol for Proteomic Plant Sample Preparation Prior LC-MS/MS. FRONTIERS IN PLANT SCIENCE 2021; 12:635550. [PMID: 33777071 PMCID: PMC7988192 DOI: 10.3389/fpls.2021.635550] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 02/17/2021] [Indexed: 05/25/2023]
Abstract
Quantitative protein extraction from biological samples, as well as contaminants removal before LC-MS/MS, is fundamental for the successful bottom-up proteomic analysis. Four sample preparation methods, including the filter-aided sample preparation (FASP), two single-pot solid-phase-enhanced sample preparations (SP3) on carboxylated or HILIC paramagnetic beads, and protein suspension trapping method (S-Trap) were evaluated for SDS removal and protein digestion from Arabidopsis thaliana (AT) lysate. Finally, the optimized carboxylated SP3 workflow was benchmarked closely against the routine FASP. Ultimately, LC-MS/MS analyses revealed that regarding the number of identifications, number of missed cleavages, proteome coverage, repeatability, reduction of handling time, and cost per assay, the SP3 on carboxylated magnetic particles proved to be the best alternative for SDS and other contaminants removal from plant sample lysate. A robust and efficient 2-h SP3 protocol for a wide range of protein input is presented, benefiting from no need to adjust the amount of beads, binding and rinsing conditions, or digestion parameters.
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Affiliation(s)
- Kamil Mikulášek
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czechia
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czechia
| | - Hana Konečná
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czechia
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czechia
| | - David Potěšil
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czechia
| | - Renata Holánková
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czechia
| | - Jan Havliš
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czechia
| | - Zbyněk Zdráhal
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czechia
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czechia
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21
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Ju Y, Kelly HG, Dagley LF, Reynaldi A, Schlub TE, Spall SK, Bell CA, Cui J, Mitchell AJ, Lin Z, Wheatley AK, Thurecht KJ, Davenport MP, Webb AI, Caruso F, Kent SJ. Person-Specific Biomolecular Coronas Modulate Nanoparticle Interactions with Immune Cells in Human Blood. ACS NANO 2020; 14:15723-15737. [PMID: 33112593 DOI: 10.1021/acsnano.0c06679] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
When nanoparticles interact with human blood, a multitude of plasma components adsorb onto the surface of the nanoparticles, forming a biomolecular corona. Corona composition is known to be influenced by the chemical composition of nanoparticles. In contrast, the possible effects of variations in the human blood proteome between healthy individuals on the formation of the corona and its subsequent interactions with immune cells in blood are unknown. Herein, we prepared and examined a matrix of 11 particles (including organic and inorganic particles of three sizes and five surface chemistries) and plasma samples from 23 healthy donors to form donor-specific biomolecular coronas (personalized coronas) and investigated the impact of the personalized coronas on particle interactions with immune cells in human blood. Among the particles examined, poly(ethylene glycol) (PEG)-coated mesoporous silica (MS) particles, irrespective of particle size (800, 450, or 100 nm in diameter), displayed the widest range (up to 60-fold difference) of donor-dependent variance in immune cell association. In contrast, PEG particles (after MS core removal) of 860, 518, or 133 nm in diameter displayed consistent stealth behavior (negligible cell association), irrespective of plasma donor. For comparison, clinically relevant PEGylated doxorubicin-encapsulated liposomes (Doxil) (74 nm in diameter) showed significant variance in association with monocytes and B cells across all plasma donors studied. An in-depth proteomic analysis of each biomolecular corona studied was performed, and the results were compared against the nanoparticle-blood cell association results, with individual variance in the proteome driving differential association with specific immune cell types. We identified key immunoglobulin and complement proteins that explicitly enriched or depleted within the corona and which strongly correlated with the cell association pattern observed across the 23 donors. This study demonstrates how plasma variance in healthy individuals significantly influences the blood immune cell interactions of nanoparticles.
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Affiliation(s)
- Yi Ju
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, and the Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Hannah G Kelly
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Laura F Dagley
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Arnold Reynaldi
- Infection Analytics Program, Kirby Institute for Infection and Immunity, University of New South Wales Australia, Sydney, New South Wales 2052, Australia
| | - Timothy E Schlub
- Sydney School of Public Health, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Sukhdeep K Spall
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Craig A Bell
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Centre for Advanced Imaging, Australian Institute for Bioengineering and Nanotechnology, ARC Training Centre for Innovation in Biomedical Imaging Technology, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Jiwei Cui
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, and the Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia
- Key Laboratory of Colloid and Interface Chemistry of the Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Andrew J Mitchell
- Department of Chemical Engineering, Materials Characterisation and Fabrication Platform, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Zhixing Lin
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, and the Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Adam K Wheatley
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Kristofer J Thurecht
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Centre for Advanced Imaging, Australian Institute for Bioengineering and Nanotechnology, ARC Training Centre for Innovation in Biomedical Imaging Technology, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Miles P Davenport
- Infection Analytics Program, Kirby Institute for Infection and Immunity, University of New South Wales Australia, Sydney, New South Wales 2052, Australia
| | - Andrew I Webb
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Frank Caruso
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, and the Department of Chemical Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Stephen J Kent
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria 3010, Australia
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22
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Thomas SL, Thacker JB, Schug KA, Maráková K. Sample preparation and fractionation techniques for intact proteins for mass spectrometric analysis. J Sep Sci 2020; 44:211-246. [DOI: 10.1002/jssc.202000936] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 10/28/2020] [Accepted: 10/29/2020] [Indexed: 12/17/2022]
Affiliation(s)
- Shannon L. Thomas
- Department of Chemistry & Biochemistry The University of Texas Arlington Arlington Texas USA
| | - Jonathan B. Thacker
- Department of Chemistry & Biochemistry The University of Texas Arlington Arlington Texas USA
| | - Kevin A. Schug
- Department of Chemistry & Biochemistry The University of Texas Arlington Arlington Texas USA
| | - Katarína Maráková
- Department of Pharmaceutical Analysis and Nuclear Pharmacy Faculty of Pharmacy Comenius University in Bratislava Bratislava Slovakia
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23
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Foers AD, Dagley LF, Chatfield S, Webb AI, Cheng L, Hill AF, Wicks IP, Pang KC. Proteomic analysis of extracellular vesicles reveals an immunogenic cargo in rheumatoid arthritis synovial fluid. Clin Transl Immunology 2020; 9:e1185. [PMID: 33204424 PMCID: PMC7648259 DOI: 10.1002/cti2.1185] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 08/12/2020] [Accepted: 09/09/2020] [Indexed: 02/06/2023] Open
Abstract
Objectives Extracellular vesicles (EVs) from rheumatoid arthritis (RA) synovial fluid (SF) have been reported to stimulate the release of pro-inflammatory mediators from recipient cells. We recently developed a size exclusion chromatography (SEC)-based method for EV isolation capable of high-quality enrichments from human SF. Here, we employed this method to accurately characterise the SF EV proteome and investigate potential contributions to inflammatory pathways in RA. Methods Using our SEC-based approach, SF EVs were purified from the joints of RA patients classified as having high-level (n = 7) or low-level inflammation (n = 5), and from osteoarthritis (OA) patients (n = 5). Protein profiles were characterised by mass spectrometry. Potential contributions of EV proteins to pathological pathways and differences in protein expression between disease groups were investigated. Results Synovial fluid EVs were present at higher concentrations in RA joints with high-level inflammation (P-value = 0.004) but were smaller in diameter (P-value = 0.03) than in low-level inflammation. In total, 1058 SF EV proteins were identified by mass spectrometry analysis. Neutrophil and fibroblast markers were overrepresented in all disease groups. Numerous proteins with potential to modulate inflammatory and immunological processes were detected, including nine citrullinated peptides. Forty-five and 135 EV-associated proteins were significantly elevated in RA joints with high-level inflammation than in RA joints with low-level inflammation and OA joints, respectively. Gene ontology analysis revealed significant enrichment for proteins associated with 'neutrophil degranulation' within SF EVs from RA joints with high-level inflammation. Conclusion Our results provide new information about SF EVs and insight into how EVs might contribute to the perpetuation of RA.
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Affiliation(s)
- Andrew D Foers
- The Walter and Eliza Hall Institute of Medical Research Parkville VIC Australia.,Department of Medical Biology University of Melbourne Parkville VIC Australia
| | - Laura F Dagley
- The Walter and Eliza Hall Institute of Medical Research Parkville VIC Australia.,Department of Medical Biology University of Melbourne Parkville VIC Australia
| | - Simon Chatfield
- The Walter and Eliza Hall Institute of Medical Research Parkville VIC Australia.,Department of Medical Biology University of Melbourne Parkville VIC Australia.,Department of Rheumatology Royal Melbourne Hospital Parkville VIC Australia
| | - Andrew I Webb
- The Walter and Eliza Hall Institute of Medical Research Parkville VIC Australia.,Department of Medical Biology University of Melbourne Parkville VIC Australia
| | - Lesley Cheng
- Department of Biochemistry and Genetics La Trobe Institute for Molecular Science La Trobe University Bundoora VIC Australia
| | - Andrew F Hill
- Department of Biochemistry and Genetics La Trobe Institute for Molecular Science La Trobe University Bundoora VIC Australia
| | - Ian P Wicks
- The Walter and Eliza Hall Institute of Medical Research Parkville VIC Australia.,Department of Medical Biology University of Melbourne Parkville VIC Australia.,Department of Rheumatology Royal Melbourne Hospital Parkville VIC Australia
| | - Ken C Pang
- The Walter and Eliza Hall Institute of Medical Research Parkville VIC Australia.,Murdoch Children's Research Institute Parkville VIC Australia.,Department of Paediatrics University of Melbourne Parkville VIC Australia.,Department of Adolescent Medicine Royal Children's Hospital. Parkville VIC Australia
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24
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McWilliam HEG, Mak JYW, Awad W, Zorkau M, Cruz-Gomez S, Lim HJ, Yan Y, Wormald S, Dagley LF, Eckle SBG, Corbett AJ, Liu H, Li S, Reddiex SJJ, Mintern JD, Liu L, McCluskey J, Rossjohn J, Fairlie DP, Villadangos JA. Endoplasmic reticulum chaperones stabilize ligand-receptive MR1 molecules for efficient presentation of metabolite antigens. Proc Natl Acad Sci U S A 2020; 117:24974-24985. [PMID: 32958637 PMCID: PMC7547156 DOI: 10.1073/pnas.2011260117] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The antigen-presenting molecule MR1 (MHC class I-related protein 1) presents metabolite antigens derived from microbial vitamin B2 synthesis to activate mucosal-associated invariant T (MAIT) cells. Key aspects of this evolutionarily conserved pathway remain uncharacterized, including where MR1 acquires ligands and what accessory proteins assist ligand binding. We answer these questions by using a fluorophore-labeled stable MR1 antigen analog, a conformation-specific MR1 mAb, proteomic analysis, and a genome-wide CRISPR/Cas9 library screen. We show that the endoplasmic reticulum (ER) contains a pool of two unliganded MR1 conformers stabilized via interactions with chaperones tapasin and tapasin-related protein. This pool is the primary source of MR1 molecules for the presentation of exogenous metabolite antigens to MAIT cells. Deletion of these chaperones reduces the ER-resident MR1 pool and hampers antigen presentation and MAIT cell activation. The MR1 antigen-presentation pathway thus co-opts ER chaperones to fulfill its unique ability to present exogenous metabolite antigens captured within the ER.
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Affiliation(s)
- Hamish E G McWilliam
- Department of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia;
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Bio21 Molecular Science and Biotechnology Institute, Parkville, VIC 3010, Australia
| | - Jeffrey Y W Mak
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Wael Awad
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, VIC 3800, Australia
| | - Matthew Zorkau
- Department of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Sebastian Cruz-Gomez
- Department of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Hui Jing Lim
- Department of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Yuting Yan
- Department of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Sam Wormald
- Division of Systems Biology and Personalised Medicine, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Laura F Dagley
- Division of Systems Biology and Personalised Medicine, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Sidonia B G Eckle
- Department of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Alexandra J Corbett
- Department of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Haiyin Liu
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Bio21 Molecular Science and Biotechnology Institute, Parkville, VIC 3010, Australia
| | - Shihan Li
- Department of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Parkville, VIC 3010, Australia
| | - Scott J J Reddiex
- Department of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Parkville, VIC 3010, Australia
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC 3052, Australia
| | - Justine D Mintern
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Bio21 Molecular Science and Biotechnology Institute, Parkville, VIC 3010, Australia
| | - Ligong Liu
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, The University of Queensland, Brisbane, QLD 4072, Australia
| | - James McCluskey
- Department of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Jamie Rossjohn
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, VIC 3800, Australia
- Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, CF14 4XN Cardiff, United Kingdom
| | - David P Fairlie
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia;
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Jose A Villadangos
- Department of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia;
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Bio21 Molecular Science and Biotechnology Institute, Parkville, VIC 3010, Australia
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25
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Zecha J, Lee CY, Bayer FP, Meng C, Grass V, Zerweck J, Schnatbaum K, Michler T, Pichlmair A, Ludwig C, Kuster B. Data, Reagents, Assays and Merits of Proteomics for SARS-CoV-2 Research and Testing. Mol Cell Proteomics 2020; 19:1503-1522. [PMID: 32591346 PMCID: PMC7780043 DOI: 10.1074/mcp.ra120.002164] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 06/26/2020] [Indexed: 12/14/2022] Open
Abstract
As the COVID-19 pandemic continues to spread, thousands of scientists around the globe have changed research direction to understand better how the virus works and to find out how it may be tackled. The number of manuscripts on preprint servers is soaring and peer-reviewed publications using MS-based proteomics are beginning to emerge. To facilitate proteomic research on SARS-CoV-2, the virus that causes COVID-19, this report presents deep-scale proteomes (10,000 proteins; >130,000 peptides) of common cell line models, notably Vero E6, Calu-3, Caco-2, and ACE2-A549 that characterize their protein expression profiles including viral entry factors such as ACE2 or TMPRSS2. Using the 9 kDa protein SRP9 and the breast cancer oncogene BRCA1 as examples, we show how the proteome expression data can be used to refine the annotation of protein-coding regions of the African green monkey and the Vero cell line genomes. Monitoring changes of the proteome on viral infection revealed widespread expression changes including transcriptional regulators, protease inhibitors, and proteins involved in innate immunity. Based on a library of 98 stable-isotope labeled synthetic peptides representing 11 SARS-CoV-2 proteins, we developed PRM (parallel reaction monitoring) assays for nano-flow and micro-flow LC-MS/MS. We assessed the merits of these PRM assays using supernatants of virus-infected Vero E6 cells and challenged the assays by analyzing two diagnostic cohorts of 24 (+30) SARS-CoV-2 positive and 28 (+9) negative cases. In light of the results obtained and including recent publications or manuscripts on preprint servers, we critically discuss the merits of MS-based proteomics for SARS-CoV-2 research and testing.
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Affiliation(s)
- Jana Zecha
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Chien-Yun Lee
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Florian P Bayer
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Chen Meng
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich, Freising, Germany
| | - Vincent Grass
- Institute of Virology, School of Medicine, Technical University of Munich, Munich, Germany; German Center for Infection Research (DZIF), Munich partner site, Germany
| | | | | | - Thomas Michler
- Institute of Virology, School of Medicine, Technical University of Munich, Munich, Germany
| | - Andreas Pichlmair
- Institute of Virology, School of Medicine, Technical University of Munich, Munich, Germany; German Center for Infection Research (DZIF), Munich partner site, Germany
| | - Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich, Freising, Germany.
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany; Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich, Freising, Germany.
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26
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Menkhorst E, Zhou W, Santos LL, Delforce S, So T, Rainczuk K, Loke H, Syngelaki A, Varshney S, Williamson N, Pringle K, Young MJ, Nicolaides KH, St-Pierre Y, Dimitriadis E. Galectin-7 Impairs Placentation and Causes Preeclampsia Features in Mice. Hypertension 2020; 76:1185-1194. [PMID: 32862708 DOI: 10.1161/hypertensionaha.120.15313] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Preeclampsia is a serious pregnancy-induced disorder unique to humans. The etiology of preeclampsia is poorly understood; however, poor placental formation is thought causal. Galectin-7 is produced by trophoblast and is elevated in first-trimester serum of women who subsequently develop preeclampsia. We hypothesized that elevated placental galectin-7 may be causative of preeclampsia. Here, we demonstrated increased galectin-7 production in chorionic villous samples from women who subsequently develop preterm preeclampsia compared with uncomplicated pregnancies. In vitro, galectin-7 impaired human first-trimester trophoblast outgrowth, increased placental production of the antiangiogenic sFlt-1 splice variant, sFlt-1-e15a, and reduced placental production and secretion of ADAM12 (a disintegrin and metalloproteinase12) and angiotensinogen. In vivo, galectin-7 administration (E8-E12) to pregnant mice caused elevated systolic blood pressure, albuminuria, impaired placentation (reduced labyrinth vascular branching, impaired decidual spiral artery remodeling, and a proinflammatory placental state demonstrated by elevated IL1β, IL6 and reduced IL10), and dysregulated expression of renin-angiotensin system components in the placenta, decidua, and kidney, including angiotensinogen, prorenin, and the angiotensin II type 1 receptor. Collectively, this study demonstrates that elevated galectin-7 during placental formation contributes to abnormal placentation and suggests that it leads to the development of preeclampsia via altering placental production of sFlt-1 and renin-angiotensin system components. Targeting galectin-7 may be a new treatment option for preeclampsia.
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Affiliation(s)
- Ellen Menkhorst
- From the Department of Obstetrics and Gynaecology, The University of Melbourne, Parkville, VIC, Australia (E.M., W.Z., L.L.S., T.S., E.D.).,Gynaecology Research Centre, Royal Women's Hospital, Parkville, VIC, Australia (E.M., W.Z., L.L.S., T.S., E.D.).,Centre for Reproductive Health, Hudson Institute of Medical Research, Clayton, VIC, Australia (E.M., K.R., H.L., E.D.)
| | - Wei Zhou
- From the Department of Obstetrics and Gynaecology, The University of Melbourne, Parkville, VIC, Australia (E.M., W.Z., L.L.S., T.S., E.D.).,Gynaecology Research Centre, Royal Women's Hospital, Parkville, VIC, Australia (E.M., W.Z., L.L.S., T.S., E.D.)
| | - Leilani L Santos
- From the Department of Obstetrics and Gynaecology, The University of Melbourne, Parkville, VIC, Australia (E.M., W.Z., L.L.S., T.S., E.D.).,Gynaecology Research Centre, Royal Women's Hospital, Parkville, VIC, Australia (E.M., W.Z., L.L.S., T.S., E.D.)
| | - Sarah Delforce
- School of Biomedical Sciences and Pharmacy (S.D., K.P.), University of Newcastle, NSW, Australia.,Priority Research Centre for Reproductive Sciences (S.D., K.P.), University of Newcastle, NSW, Australia.,Pregnancy and Reproduction Program, Hunter Medical Research Institute, Newcastle, NSW, Australia (S.D., K.P.)
| | - Teresa So
- From the Department of Obstetrics and Gynaecology, The University of Melbourne, Parkville, VIC, Australia (E.M., W.Z., L.L.S., T.S., E.D.).,Gynaecology Research Centre, Royal Women's Hospital, Parkville, VIC, Australia (E.M., W.Z., L.L.S., T.S., E.D.)
| | - Kate Rainczuk
- Centre for Reproductive Health, Hudson Institute of Medical Research, Clayton, VIC, Australia (E.M., K.R., H.L., E.D.)
| | - Hannah Loke
- Centre for Reproductive Health, Hudson Institute of Medical Research, Clayton, VIC, Australia (E.M., K.R., H.L., E.D.)
| | - Argyro Syngelaki
- Harris Birthright Research Centre for Fetal Medicine, King's College Hospital, London, United Kingdom (A.S., K.H.N.)
| | - Swati Varshney
- Melbourne Mass Spectrometry and Proteomics Facility, Bio21 Molecular Science & Biotechnology Institute, The University of Melbourne, VIC, Australia (S.V., N.W.)
| | - Nicholas Williamson
- Melbourne Mass Spectrometry and Proteomics Facility, Bio21 Molecular Science & Biotechnology Institute, The University of Melbourne, VIC, Australia (S.V., N.W.)
| | - Kirsty Pringle
- School of Biomedical Sciences and Pharmacy (S.D., K.P.), University of Newcastle, NSW, Australia.,Priority Research Centre for Reproductive Sciences (S.D., K.P.), University of Newcastle, NSW, Australia.,Pregnancy and Reproduction Program, Hunter Medical Research Institute, Newcastle, NSW, Australia (S.D., K.P.)
| | - Morag J Young
- Centre for Endocrinology and Metabolism, Hudson Institute of Medical Research, Clayton, VIC, Australia (M.J.Y.).,Baker Heart & Diabetes Institute, Prahran, VIC, Australia (M.J.Y.)
| | - Kypros H Nicolaides
- Harris Birthright Research Centre for Fetal Medicine, King's College Hospital, London, United Kingdom (A.S., K.H.N.)
| | - Yves St-Pierre
- INRS-Institut Armand-Frappier, Laval, QC, Canada (Y.S.-P.)
| | - Eva Dimitriadis
- From the Department of Obstetrics and Gynaecology, The University of Melbourne, Parkville, VIC, Australia (E.M., W.Z., L.L.S., T.S., E.D.).,Gynaecology Research Centre, Royal Women's Hospital, Parkville, VIC, Australia (E.M., W.Z., L.L.S., T.S., E.D.).,Centre for Reproductive Health, Hudson Institute of Medical Research, Clayton, VIC, Australia (E.M., K.R., H.L., E.D.).,Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia (E.D.)
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27
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Källsten M, Ghorasaini M, Hartmann R, Lehmann F, Bergquist J, Kovac L, Lind SB. Magnetic Beads for Desalting of Monoclonal Antibodies and Antibody-Drug Conjugates. Anal Chem 2020; 92:9001-9007. [PMID: 32441508 DOI: 10.1021/acs.analchem.0c01106] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Characterization of antibody-drug conjugates (ADCs) using mass spectrometry (MS) is important in drug discovery and formulation development and as part of the quality control processes. To facilitate electrospray ionization (ESI) and produce high-quality mass spectra, common components of storage solutions for monoclonal antibodies (mAbs) and ADCs, such as nonvolatile phosphate-buffered saline (PBS), should be replaced before analysis. Centrifugal spin-type kits are extensively used for the desalting or buffer-exchange of mAbs and ADCs samples. The commercially available kits commonly require at least 100 μL of a sample at 1 mg/mL for optimal recovery. However, most ESI-MS based analyses require no more than 25 μg of protein for triplicate injection. In this study, we present a novel method for desalting of ADCs and mAbs building on the SP3 approach with nonfunctionalized carboxylate coated magnetic beads without affinity ligands. The analytes bind to the hydrophilic beads upon the addition of organic solvent, and various solutions of volatile salts or acids can be used in the elution step. The optimized protocol allowed for 88% recovery of ADC at a 25 μL sample volume and 90% recovery at 100 μL. More than 90% of the salts were removed using a process of 20 min. The intra- and interday precision showed little variation with an RSD of 1% and 2%, respectively. The compatibility of this new workflow with low sample volumes is highly valuable since a smaller fraction of the sample is wasted for analysis of the expensive analytes, without compromising recovery.
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Affiliation(s)
- Malin Källsten
- Department of Chemistry-BMC, Analytical Chemistry, Uppsala University, Box 599, Husargatan 3, SE-75124 Uppsala, Sweden.,Recipharm OT Chemistry AB, Virdings Allé 18, SE-754 50 Uppsala, Sweden
| | - Mohan Ghorasaini
- Department of Chemistry-BMC, Analytical Chemistry, Uppsala University, Box 599, Husargatan 3, SE-75124 Uppsala, Sweden
| | - Rafael Hartmann
- Department of Medicinal Chemistry, Uppsala University, Box 574, Husargatan 3, SE-751 23 Uppsala, Sweden
| | - Fredrik Lehmann
- Oncopeptides AB, Västra Trädgårdsgatan 15, 111 53 Stockholm, Sweden
| | - Jonas Bergquist
- Department of Chemistry-BMC, Analytical Chemistry, Uppsala University, Box 599, Husargatan 3, SE-75124 Uppsala, Sweden
| | - Lucia Kovac
- Recipharm OT Chemistry AB, Virdings Allé 18, SE-754 50 Uppsala, Sweden
| | - Sara Bergström Lind
- Department of Chemistry-BMC, Analytical Chemistry, Uppsala University, Box 599, Husargatan 3, SE-75124 Uppsala, Sweden
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28
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High-throughput proteotyping of bacterial isolates by double barrel chromatography-tandem mass spectrometry based on microplate paramagnetic beads and phylopeptidomics. J Proteomics 2020; 226:103887. [PMID: 32619772 DOI: 10.1016/j.jprot.2020.103887] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 06/19/2020] [Accepted: 06/25/2020] [Indexed: 12/18/2022]
Abstract
Tandem mass spectrometry-based proteotyping of microorganisms presents several advantages over whole-cell MALDI-TOF mass spectrometry: because a larger number of signals are recorded with better accuracy and precision, the approach allows for the identification of microorganisms at more resolved taxonomic levels, and can easily manage complex samples. Additionally, the use of SP3 paramagnetic beads for cell lysis and protein cleanup simplifies sample preparation for proteotyping. Based on these features, we have developed and tested a 96-well plate platform for high-throughput proteotyping of a large variety of bacteria. We evaluated the performance of the platform in terms of bacterial load and found no cross-contamination between wells. Likewise, phylopeptidomics analysis revealed no alteration in the relative quantifications of microorganisms. Finally, we applied this new format for rapid proteotyping of a large set of dental isolates using double-barrel chromatography coupled to tandem mass spectrometry, which maximizes the number of spectra per unit of time. The procedure allowed us to establish whether these isolates were pure strains or mixtures of strains and to identify the microorganisms at the most resolved taxonomic level. SIGNIFICANCE: The rapid and accurate identification of microorganisms is a clinical priority in medical diagnostics; however, specimens containing mixtures of microorganisms are difficult to analyze and the procedure is time-consuming. Tandem mass spectrometry proteotyping allows the fast identification of complex mixtures of microorganisms, known or unknown, and can also establish the biomass ratio of each component. We describe here a new workflow for preparing microbial samples in a 96-well-plate format for tandem mass spectrometry proteotyping and document its advantages and limitations. We demonstrate that this new format coupled to a highly efficient double-barrel LC-MS/MS system allows proteotyping of 96 isolates in 55 h.
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29
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Yang Z, Shen X, Chen D, Sun L. Toward a Universal Sample Preparation Method for Denaturing Top-Down Proteomics of Complex Proteomes. J Proteome Res 2020; 19:3315-3325. [PMID: 32419461 DOI: 10.1021/acs.jproteome.0c00226] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
A universal and standardized sample preparation method becomes vital for denaturing top-down proteomics (dTDP) to advance the scale and accuracy of proteoform delineation in complex biological systems. It needs to have high protein recovery, minimum bias, good reproducibility, and compatibility with downstream mass spectrometry (MS) analysis. Here, we employed a lysis buffer containing sodium dodecyl sulfate for extracting proteoforms from cells and, for the first time, compared membrane ultrafiltration (MU), chloroform-methanol precipitation (CMP), and single-spot solid-phase sample preparation using magnetic beads (SP3) for proteoform cleanup for dTDP. The MU method outperformed CMP and SP3 methods, resulting in high and reproducible protein recovery from both Escherichia coli cell (59 ± 3%) and human HepG2 cell (86 ± 5%) samples without a significant bias. Single-shot capillary zone electrophoresis (CZE)-MS/MS analyses of the prepared E. coli and HepG2 cell samples using the MU method identified 821 and 516 proteoforms, respectively. Nearly 30 and 50% of the identified E. coli and HepG2 proteins are membrane proteins. CZE-MS/MS identified 94 histone proteoforms from the HepG2 sample with various post-translational modifications, including acetylation, methylation, and phosphorylation. Our results suggest that combining the SDS-based protein extraction and the MU-based protein cleanup could be a universal sample preparation method for dTDP. The MS raw data have been deposited to the ProteomeXchange Consortium with the data set identifier PXD018248.
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Affiliation(s)
- Zhichang Yang
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, Michigan 48824 United States
| | - Xiaojing Shen
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, Michigan 48824 United States
| | - Daoyang Chen
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, Michigan 48824 United States
| | - Liangliang Sun
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, Michigan 48824 United States
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30
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Bedford JG, Infusini G, Dagley LF, Villalon-Letelier F, Zheng MZM, Bennett-Wood V, Reading PC, Wakim LM. Airway Exosomes Released During Influenza Virus Infection Serve as a Key Component of the Antiviral Innate Immune Response. Front Immunol 2020; 11:887. [PMID: 32477358 PMCID: PMC7236881 DOI: 10.3389/fimmu.2020.00887] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 04/16/2020] [Indexed: 12/21/2022] Open
Abstract
Exosomes are extracellular vesicles secreted by cells that have an important biological function in intercellular communication by transferring biologically active proteins, lipids, and RNAs to neighboring or distant cells. While a role for exosomes in antimicrobial defense has recently emerged, currently very little is known regarding the nature and functional relevance of exosomes generated in vivo, particularly during an active viral infection. Here, we characterized exosomes released into the airways during influenza virus infection. We show that these vesicles dynamically change in protein composition over the course of infection, increasing expression of host proteins with known anti-influenza activity, and viral proteins with the potential to trigger host immune responses. We show that exosomes released into the airways during influenza virus infection trigger pulmonary inflammation and carry viral antigen that can be utilized by antigen presenting cells to drive the induction of a cellular immune response. Moreover, we show that attachment factors for influenza virus, namely α2,3 and α2,6-linked sialic acids, are present on the surface of airway exosomes and these vesicles have the ability to neutralize influenza virus, thereby preventing the virus from binding and entering target cells. These data reveal a novel role for airway exosomes in the antiviral innate immune defense against influenza virus infection.
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Affiliation(s)
- James G Bedford
- Department of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Giuseppe Infusini
- Department of Medical Biology, The Walter and Eliza Hall Institute of Medical Research, The University of Melbourne, Melbourne, VIC, Australia
| | - Laura F Dagley
- Department of Medical Biology, The Walter and Eliza Hall Institute of Medical Research, The University of Melbourne, Melbourne, VIC, Australia
| | - Fernando Villalon-Letelier
- Department of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Ming Z M Zheng
- Department of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Vicki Bennett-Wood
- Department of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Patrick C Reading
- Department of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.,WHO Collaborating Centre for Reference and Research on Influenza, Victorian Infectious Diseases Reference Laboratory, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Linda M Wakim
- Department of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
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31
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Zacchi LF, Recinos DR, Otte E, Aitken C, Hunt T, Sandford V, Lee YY, Schulz BL, Howard CB. S-Trap Eliminates Cell Culture Media Polymeric Surfactants for Effective Proteomic Analysis of Mammalian Cell Bioreactor Supernatants. J Proteome Res 2020; 19:2149-2158. [DOI: 10.1021/acs.jproteome.0c00106] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lucia F. Zacchi
- ARC Training Centre for Biopharmaceutical Innovation, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Dinora Roche Recinos
- ARC Training Centre for Biopharmaceutical Innovation, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, Queensland 4072, Australia
- CSL Limited, Parkville, Victoria 3052, Australia
| | - Ellen Otte
- CSL Limited, Parkville, Victoria 3052, Australia
| | | | - Tony Hunt
- CSL Limited, Parkville, Victoria 3052, Australia
| | | | - Yih Yean Lee
- CSL Limited, Parkville, Victoria 3052, Australia
| | - Benjamin L. Schulz
- ARC Training Centre for Biopharmaceutical Innovation, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, Queensland 4072, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Christopher B. Howard
- ARC Training Centre for Biopharmaceutical Innovation, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, Queensland 4072, Australia
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32
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Müller T, Kalxdorf M, Longuespée R, Kazdal DN, Stenzinger A, Krijgsveld J. Automated sample preparation with SP3 for low-input clinical proteomics. Mol Syst Biol 2020; 16:e9111. [PMID: 32129943 PMCID: PMC6966100 DOI: 10.15252/msb.20199111] [Citation(s) in RCA: 134] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Revised: 12/04/2019] [Accepted: 12/05/2019] [Indexed: 12/14/2022] Open
Abstract
High-throughput and streamlined workflows are essential in clinical proteomics for standardized processing of samples from a variety of sources, including fresh-frozen tissue, FFPE tissue, or blood. To reach this goal, we have implemented single-pot solid-phase-enhanced sample preparation (SP3) on a liquid handling robot for automated processing (autoSP3) of tissue lysates in a 96-well format. AutoSP3 performs unbiased protein purification and digestion, and delivers peptides that can be directly analyzed by LCMS, thereby significantly reducing hands-on time, reducing variability in protein quantification, and improving longitudinal reproducibility. We demonstrate the distinguishing ability of autoSP3 to process low-input samples, reproducibly quantifying 500-1,000 proteins from 100 to 1,000 cells. Furthermore, we applied this approach to a cohort of clinical FFPE pulmonary adenocarcinoma (ADC) samples and recapitulated their separation into known histological growth patterns. Finally, we integrated autoSP3 with AFA ultrasonication for the automated end-to-end sample preparation and LCMS analysis of 96 intact tissue samples. Collectively, this constitutes a generic, scalable, and cost-effective workflow with minimal manual intervention, enabling reproducible tissue proteomics in a broad range of clinical and non-clinical applications.
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Affiliation(s)
- Torsten Müller
- German Cancer Research Center (DKFZ)HeidelbergGermany
- Medical FacultyHeidelberg UniversityHeidelbergGermany
| | - Mathias Kalxdorf
- German Cancer Research Center (DKFZ)HeidelbergGermany
- EMBLHeidelbergGermany
| | - Rémi Longuespée
- Department of Clinical Pharmacology and PharmacoepidemiologyHeidelberg UniversityHeidelbergGermany
| | - Daniel N Kazdal
- Institute of PathologyHeidelberg UniversityHeidelbergGermany
| | | | - Jeroen Krijgsveld
- German Cancer Research Center (DKFZ)HeidelbergGermany
- Medical FacultyHeidelberg UniversityHeidelbergGermany
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33
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Rautela J, Dagley LF, de Oliveira CC, Schuster IS, Hediyeh-Zadeh S, Delconte RB, Cursons J, Hennessy R, Hutchinson DS, Harrison C, Kita B, Vivier E, Webb AI, Degli-Esposti MA, Davis MJ, Huntington ND, Souza-Fonseca-Guimaraes F. Therapeutic blockade of activin-A improves NK cell function and antitumor immunity. Sci Signal 2019; 12:12/596/eaat7527. [PMID: 31455725 DOI: 10.1126/scisignal.aat7527] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Natural killer (NK) cells are innate lymphocytes that play a major role in immunosurveillance against tumor initiation and metastatic spread. The signals and checkpoints that regulate NK cell fitness and function in the tumor microenvironment are not well defined. Transforming growth factor-β (TGF-β) is a suppressor of NK cells that inhibits interleukin-15 (IL-15)-dependent signaling events and increases the abundance of receptors that promote tissue residency. Here, we showed that NK cells express the type I activin receptor ALK4, which, upon binding to its ligand activin-A, phosphorylated SMAD2/3 to suppress IL-15-mediated NK cell metabolism. Activin-A impaired human and mouse NK cell proliferation and reduced the production of granzyme B to impair tumor killing. Similar to TGF-β, activin-A also induced SMAD2/3 phosphorylation and stimulated NK cells to increase their cell surface expression of several markers of ILC1 cells. Activin-A also induced these changes in TGF-β receptor-deficient NK cells, suggesting that activin-A and TGF-β stimulate independent pathways that drive SMAD2/3-mediated NK cell suppression. Last, inhibition of activin-A by follistatin substantially slowed orthotopic melanoma growth in mice. These data highlight the relevance of examining TGF-β-independent SMAD2/3 signaling mechanisms as a therapeutic axis to relieve NK cell suppression and promote antitumor immunity.
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Affiliation(s)
- Jai Rautela
- Division of Molecular Immunology, The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria 3052, Australia.,Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Laura F Dagley
- Systems Biology and Personalized Medicine Division, The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Carolina C de Oliveira
- Laboratório de Células Inflamatórias e Neoplásicas, Departamento de Biologia Celular, SCB, Centro Politecnico, Universidade Federal do Paraná, Curitiba, CEP 81531-980, PR, Brazil
| | - Iona S Schuster
- Immunology and Virology Program, Centre for Ophthalmology and Visual Science, University of Western Australia, Crawley, Western Australia, Australia.,Centre for Experimental Immunology, Lions Eye Institute, Nedlands, Western Australia, Australia.,Infection and Immunity Program and Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Soroor Hediyeh-Zadeh
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology and Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Rebecca B Delconte
- Division of Molecular Immunology, The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Joseph Cursons
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology and Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Robert Hennessy
- Division of Molecular Immunology, The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Dana S Hutchinson
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Craig Harrison
- Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Badia Kita
- Paranta Biosciences Limited, Melbourne, Victoria 3004, Australia
| | - Eric Vivier
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, Inserm, CNRS, 13288 Marseille, France
| | - Andrew I Webb
- Systems Biology and Personalized Medicine Division, The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Mariapia A Degli-Esposti
- Immunology and Virology Program, Centre for Ophthalmology and Visual Science, University of Western Australia, Crawley, Western Australia, Australia.,Centre for Experimental Immunology, Lions Eye Institute, Nedlands, Western Australia, Australia.,Infection and Immunity Program and Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Melissa J Davis
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology and Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria 3052, Australia.,Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Nicholas D Huntington
- Division of Molecular Immunology, The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria 3052, Australia.,Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Fernando Souza-Fonseca-Guimaraes
- Division of Molecular Immunology, The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria 3052, Australia. .,University of Queensland Diamantina Institute, University of Queensland, Translational Research Institute, Brisbane, Queensland, Australia
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34
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Wiśniewski JR. Filter Aided Sample Preparation - A tutorial. Anal Chim Acta 2019; 1090:23-30. [PMID: 31655642 DOI: 10.1016/j.aca.2019.08.032] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 08/13/2019] [Accepted: 08/14/2019] [Indexed: 01/08/2023]
Abstract
Filter Aided Sample Preparation (FASP) is a widely used protein processing technique in "bottom-up" proteomics. Its popularity reflects the key features of the method: its applicability to a variety of sample types and the high quality of the released peptides. Successful application of FASP requires optimized properties of sample lysate and its amount, use of ultrafiltration units with membranes having large molecular mass cut-offs and well selected conditions for protein digestion. In contrast to the majority of sample preparation methods, FASP allows digestion of proteins with a variety of enzymes and a straightforward monitoring of protein-to-peptide conversion. A unique feature of FASP is the possibility to cleave proteins in a consecutive way using several proteases and to separate peptide fractions. Understanding principles of the method gives guidance in applying FASP to different types of samples in optimization of conditions of the FASP-workflow.
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Affiliation(s)
- Jacek R Wiśniewski
- Biochemical Proteomics Group, Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, D-82152, Martinsried, Germany.
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