1
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Jiang RW, Marin LM, Jaroch K, Zhou W, Siqueira WL, Pawliszyn J. Proteomic Analysis of Human Saliva via Solid-Phase Microextraction Coupled with Liquid Chromatography-Mass Spectrometry. Anal Chem 2024; 96:5363-5367. [PMID: 38535996 DOI: 10.1021/acs.analchem.4c00307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/10/2024]
Abstract
Proteomics of human saliva samples was achieved for the first time via biocompatible solid-phase microextraction (bio-SPME) devices. Upon introduction of a porogen to a conventional C18 coating, porous C18/polyacrylonitrile (PAN) SPME blades were able to extract peptides up to 3.0 kDa and more peptides than commercial SPME blades. Following Trypsin digestion, salivary proteomic analysis was achieved via SPME-LC-MS/MS. Seven endogenous proteins were consistently identified in all saliva samples via bio-SPME. Taking advantage of this strategy, untargeted peptidomics was applied for the comparison of saliva samples between healthy and SARS-CoV-2 positive individuals. The results showed clear peptidomic differences between the viral and healthy saliva samples. This proof-of-concept study demonstrates the potential of bio-SPME-LC-MS/MS for peptidomics and proteomics in biomedical applications.
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Affiliation(s)
- Runshan W Jiang
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Lina M Marin
- College of Dentistry, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada
| | - Karol Jaroch
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
- Department of Pharmacodynamics and Molecular Pharmacology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Bydgoszcz 85-089, Poland
| | - Wei Zhou
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Walter L Siqueira
- College of Dentistry, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada
| | - Janusz Pawliszyn
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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2
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Avtanski D, Hadzi-Petrushev N, Josifovska S, Mladenov M, Reddy V. Emerging technologies in adipose tissue research. Adipocyte 2023; 12:2248673. [PMID: 37599422 PMCID: PMC10443968 DOI: 10.1080/21623945.2023.2248673] [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: 06/11/2023] [Revised: 08/03/2023] [Accepted: 08/07/2023] [Indexed: 08/22/2023] Open
Abstract
Technologies are transforming the understanding of adipose tissue as a complex and dynamic tissue that plays a critical role in energy homoeostasis and metabolic health. This mini-review provides a brief overview of the potential impact of novel technologies in biomedical research and aims to identify areas where these technologies can make the most significant contribution to adipose tissue research. It discusses the impact of cutting-edge technologies such as single-cell sequencing, multi-omics analyses, spatial transcriptomics, live imaging, 3D tissue engineering, microbiome analysis, in vivo imaging, and artificial intelligence/machine learning. As these technologies continue to evolve, we can expect them to play an increasingly important role in advancing our understanding of adipose tissue and improving the treatment of related diseases.
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Affiliation(s)
- Dimiter Avtanski
- Friedman Diabetes Institute, Lenox Hill Hospital, New York, NY, USA
- Institute of Bioelectronic Medicine, Feinstein Institutes for Medical Research, Manhasset, NY, USA
- Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, USA
| | - Nikola Hadzi-Petrushev
- Faculty of Natural Sciences and Mathematics, Institute of Biology, “Ss. Cyril and Methodius” University, Skopje, North Macedonia
| | - Slavica Josifovska
- Faculty of Natural Sciences and Mathematics, Institute of Biology, “Ss. Cyril and Methodius” University, Skopje, North Macedonia
| | - Mitko Mladenov
- Faculty of Natural Sciences and Mathematics, Institute of Biology, “Ss. Cyril and Methodius” University, Skopje, North Macedonia
| | - Varun Reddy
- New York Institute of Technology College of Osteopathic Medicine, Old Westbury, NY, USA
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3
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Álvarez-Urdiola R, Borràs E, Valverde F, Matus JT, Sabidó E, Riechmann JL. Peptidomics Methods Applied to the Study of Flower Development. Methods Mol Biol 2023; 2686:509-536. [PMID: 37540375 DOI: 10.1007/978-1-0716-3299-4_24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
Understanding the global and dynamic nature of plant developmental processes requires not only the study of the transcriptome, but also of the proteome, including its largely uncharacterized peptidome fraction. Recent advances in proteomics and high-throughput analyses of translating RNAs (ribosome profiling) have begun to address this issue, evidencing the existence of novel, uncharacterized, and possibly functional peptides. To validate the accumulation in tissues of sORF-encoded polypeptides (SEPs), the basic setup of proteomic analyses (i.e., LC-MS/MS) can be followed. However, the detection of peptides that are small (up to ~100 aa, 6-7 kDa) and novel (i.e., not annotated in reference databases) presents specific challenges that need to be addressed both experimentally and with computational biology resources. Several methods have been developed in recent years to isolate and identify peptides from plant tissues. In this chapter, we outline two different peptide extraction protocols and the subsequent peptide identification by mass spectrometry using the database search or the de novo identification methods.
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Affiliation(s)
- Raquel Álvarez-Urdiola
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, Cerdanyola del Vallès, Barcelona, Spain
| | - Eva Borràs
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Federico Valverde
- Institute for Plant Biochemistry and Photosynthesis CSIC - University of Seville, Seville, Spain
| | - José Tomás Matus
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, Cerdanyola del Vallès, Barcelona, Spain
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna, Valencia, Spain
| | - Eduard Sabidó
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - José Luis Riechmann
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, Cerdanyola del Vallès, Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
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4
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Müller T, Cremonini MA, Kliewer G, Krijgsveld J. Automated Sample Preparation for Mass Spectrometry-Based Clinical Proteomics. Methods Mol Biol 2023; 2718:181-211. [PMID: 37665461 DOI: 10.1007/978-1-0716-3457-8_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Mass spectrometry (MS)-based proteomics is a rapidly maturing discipline, thus gaining momentum for routine molecular profiling of clinical specimens to improve disease classification, diagnostics, and therapy development. Yet, hurdles need to be overcome to enhance reproducibility in preanalytical sample processing, especially in large, quantity-limited sample cohorts. Therefore, automated sonication and single-pot solid-phase-enhanced sample preparation (autoSP3) was developed as a streamlined workflow that integrates all tasks from tissue lysis and protein extraction, protein cleanup, and proteolysis. It enables the concurrent processing of 96 clinical samples of any type (fresh-frozen or FFPE tissue, liquid biopsies, or cells) on an automated liquid handling platform, which can be directly interfaced to LC-MS for proteome analysis of clinical specimens with high sensitivity, high reproducibility, and short turn-around times.
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Affiliation(s)
- Torsten Müller
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg University, Medical Faculty, Heidelberg, Germany
| | | | - Georg Kliewer
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg University, Medical Faculty, Heidelberg, Germany
| | - Jeroen Krijgsveld
- German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Heidelberg University, Medical Faculty, Heidelberg, Germany.
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5
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Spice DM, Cooper TT, Lajoie GA, Kelly GM. Never in Mitosis Kinase 2 regulation of metabolism is required for neural differentiation. Cell Signal 2022; 100:110484. [PMID: 36195199 DOI: 10.1016/j.cellsig.2022.110484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/27/2022] [Accepted: 09/28/2022] [Indexed: 11/24/2022]
Abstract
Wnt and Hh are known signalling pathways involved in neural differentiation and recent work has shown the cell cycle regulator, Never in Mitosis Kinase 2 (Nek2) is able to regulate both pathways. Despite its known function in pathway regulation, few studies have explored Nek2 within embryonic development. The P19 embryonal carcinoma cell model was used to investigate Nek2 and neural differentiation through CRISPR knockout and overexpression studies. Loss of Nek2 reduced cell proliferation in the undifferentiated state and during directed differentiation, while overexpression increased cell proliferation. Despite these changes in proliferation rates, Nek2 deficient cells maintained pluripotency markers after neural induction while Nek2 overexpressing cells lost these markers in the undifferentiated state. Nek2 deficient cells lost the ability to differentiate into both neurons and astrocytes, although Nek2 overexpressing cells enhanced neuron differentiation at the expense of astrocytes. Hh and Wnt signalling were explored, however there was no clear connection between Nek2 and these pathways causing the observed changes to differentiation phenotypes. Mass spectrometry was also used during wildtype and Nek2 knockout cell differentiation and we identified reduced electron transport chain components in the knockout population. Immunoblotting confirmed the loss of these components and additional studies showed cells lacking Nek2 were exclusively glycolytic. Interestingly, hypoxia inducible factor 1α was stabilized in these Nek2 knockout cells despite culturing them under normoxic conditions. Since neural differentiation requires a metabolic switch from glycolysis to oxidative phosphorylation, we propose a mechanism where Nek2 prevents HIF1α stabilization, thereby allowing cells to use oxidative phosphorylation to facilitate neuron and astrocyte differentiation.
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Affiliation(s)
- Danielle M Spice
- Department of Biology, Western University, 1151 Richmond Street, London, ON N6A 5B7, Canada.
| | - Tyler T Cooper
- Department of Biochemistry, Western University, 1151 Richmond Street, London, ON N6A 5C1, Canada.
| | - Gilles A Lajoie
- Department of Biochemistry, Western University, 1151 Richmond Street, London, ON N6A 5C1, Canada; Don Rix Protein Identification Facility, University of Western, Ontario, London, ON N6G 2V4, Canada.
| | - Gregory M Kelly
- Department of Biology, Western University, 1151 Richmond Street, London, ON N6A 5B7, Canada; Child Health Research Institute, 345 Westminster Ave, London, ON N6C 4V3, Canada.
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6
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Onea G, Maitland MER, Wang X, Lajoie GA, Schild-Poulter C. Distinct assemblies and interactomes of the nuclear and cytoplasmic mammalian CTLH E3 ligase complex. J Cell Sci 2022; 135:276121. [PMID: 35833506 DOI: 10.1242/jcs.259638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 06/27/2022] [Indexed: 11/20/2022] Open
Abstract
The C-terminal to LisH (CTLH) complex is a newly discovered multi-subunit E3 ubiquitin ligase whose cellular functions are poorly characterized. While some CTLH subunits have been found to localize in both the nucleus and cytoplasm of mammalian cells, differences between the compartment-specific complexes have not been explored. Here, we show that the CTLH complex forms different molecular weight complexes in nuclear and cytoplasmic fractions. Loss of WDR26 severely decreases nuclear CTLH complex subunit levels and impairs higher-order CTLH complex formation, revealing WDR26 as a critical determinant of CTLH complex nuclear stability. Through affinity purification coupled to mass spectrometry (AP-MS) of endogenous CTLH complex member RanBPM from nuclear and cytoplasmic fractions, we identified over 170 compartment-specific interactors involved in various conserved biological processes such as ribonucleoprotein biogenesis and chromatin assembly. We validated the nuclear-specific RanBPM interaction with macroH2A1 and the cytoplasmic-specific interaction with Tankyrase-1/2. Overall, this study provides critical insights into CTLH complex function and composition in both the cytoplasm and nucleus.
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Affiliation(s)
- Gabriel Onea
- Robarts Research Institute, University of Western Ontario, London, Ontario, N6A 5B7, Canada.,Department of Biochemistry, University of Western Ontario, London, Ontario, ON N6G 2V4, Canada
| | - Matthew E R Maitland
- Robarts Research Institute, University of Western Ontario, London, Ontario, N6A 5B7, Canada.,Department of Biochemistry, University of Western Ontario, London, Ontario, ON N6G 2V4, Canada.,Don Rix Protein Identification Facility, University of Western Ontario, London, Ontario, N6G 2V4, Canada
| | - Xu Wang
- Robarts Research Institute, University of Western Ontario, London, Ontario, N6A 5B7, Canada.,Department of Biochemistry, University of Western Ontario, London, Ontario, ON N6G 2V4, Canada
| | - Gilles A Lajoie
- Department of Biochemistry, University of Western Ontario, London, Ontario, ON N6G 2V4, Canada.,Don Rix Protein Identification Facility, University of Western Ontario, London, Ontario, N6G 2V4, Canada
| | - Caroline Schild-Poulter
- Robarts Research Institute, University of Western Ontario, London, Ontario, N6A 5B7, Canada.,Department of Biochemistry, University of Western Ontario, London, Ontario, ON N6G 2V4, Canada
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7
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Zheng W, Yang P, Sun C, Zhang Y. Comprehensive comparison of sample preparation workflows for proteomics. Mol Omics 2022; 18:555-567. [DOI: 10.1039/d2mo00076h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Mass spectrometry-based proteomics experiments can be subject to a large variability, which forms an obstacle to obtaining deep and accurate protein identification. Here, to obtain an optimal sample preparation workflow...
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8
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Sun R, Lyu M, Liang S, Ge W, Wang Y, Ding X, Zhang C, Zhou Y, Chen S, Chen L, Guo T. A prostate cancer tissue specific spectral library for targeted proteomic analysis. Proteomics 2021; 22:e2100147. [PMID: 34799972 DOI: 10.1002/pmic.202100147] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 10/19/2021] [Accepted: 11/03/2021] [Indexed: 11/08/2022]
Abstract
Prostate cancer is the most common cancer in males worldwide. Mass spectrometry-based targeted proteomics has demonstrated great potential in quantifying proteins from formalin-fixed paraffin-embedded (FFPE) and (fresh) frozen biopsy tissues. Here we provide a comprehensive tissue-specific spectral library for targeted proteomic analysis of prostate tissue samples. Benign and malignant FFPE prostate tissue samples were processed into peptide samples by pressure cycling technology (PCT)-assisted sample preparation, and fractionated with high-pH reversed phase liquid chromatography (RPLC). Based on data-dependent acquisition (DDA) MS analysis using a TripleTOF 6600, we built a library containing 108,533 precursors, 84,198 peptides and 9384 unique proteins (1% FDR). The applicability of the library was demonstrated in prostate specimens.
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Affiliation(s)
- Rui Sun
- Zhejiang University, Hangzhou, Zhejiang, China.,Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China.,Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Mengge Lyu
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China.,Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Shuang Liang
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China.,Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Weigang Ge
- Westlake Omics (Hangzhou) Biotechnology Co., Ltd., Hangzhou, China
| | - Yingrui Wang
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China.,Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Xuan Ding
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China.,Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Cheng Zhang
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China.,Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Yan Zhou
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China.,Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Shanjun Chen
- Westlake Omics (Hangzhou) Biotechnology Co., Ltd., Hangzhou, China
| | - Lirong Chen
- Department of Pathology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Tiannan Guo
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China.,Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
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9
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Global Comparative Label-Free Yeast Proteome Analysis by LC-MS/MS After High-pH Reversed-Phase Peptide Fractionation Using Solid-Phase Extraction Cartridges. Methods Mol Biol 2021. [PMID: 34786677 DOI: 10.1007/978-1-0716-1822-6_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
Discovery-driven comparative proteomics employing the bottom-up strategy with label-free quantification on high-resolution mass analyzers like an Orbitrap in a hybrid instrument has the capacity to reveal unique biological processes in the context of plant metabolic engineering. However, proteins are very heterogeneous in nature with a wide range of expression levels, and overall coverage may be suboptimal regarding both the number of protein identifications and sequence coverage of the identified proteins using conventional data-dependent acquisitions without sample fractionation before online nanoflow liquid chromatography-mass spectrometry (LC-MS) and tandem mass spectrometry (MS/MS). In this chapter, we detail a simple and robust method employing high-pH reversed-phase (HRP) peptide fractionation using solid-phase extraction cartridges for label-free proteomic analyses. Albeit HRP fractionation separates peptides according to their hydrophobicity like the subsequent nanoflow gradient reversed-phased LC relying on low pH mobile phase, the two methods are orthogonal. Presented here as a protocol with yeast (Saccharomyces cerevisiae) as a frequently used model organism and hydrogen peroxide to exert cellular stress and survey its impact compared to unstressed control as an example, the described workflow can be adapted to a wide range of proteome samples for applications to plant metabolic engineering research.
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10
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Biedka S, Schmidt BF, Frey NM, Boothman SM, Minden JS, Lucas A. Reversible Click Chemistry Tag for Universal Proteome Sample Preparation for Top-Down and Bottom-Up Analysis. J Proteome Res 2021; 20:4787-4800. [PMID: 34524823 DOI: 10.1021/acs.jproteome.1c00443] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Successful proteome analysis requires reliable sample preparation beginning with protein solubilization and ending with a sample free of contaminants, ready for downstream analysis. Most proteome sample preparation technologies utilize precipitation or filter-based separation, both of which have significant disadvantages. None of the current technologies are able to prepare both intact proteins or digested peptides. Here, we introduce a reversible protein tag, ProMTag, that enables whole proteome capture, cleanup, and release of intact proteins for top-down analysis. Alternatively, the addition of a novel Trypsin derivative to the workflow generates peptides for bottom-up analysis. We show that the ProMTag workflow yields >90% for intact proteins and >85% for proteome digests. For top-down analysis, ProMTag cleanup improves resolution on 2D gels; for bottom-up exploration, this methodology produced reproducible mass spectrometry results, demonstrating that the ProMTag method is a truly universal approach that produces high-quality proteome samples compatible with multiple downstream analytical techniques. Data are available via ProteomeXchange with identifier PXD027799.
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Affiliation(s)
- Stephanie Biedka
- Impact Proteomics, LLC., Pittsburgh, Pennsylvania 15206, United States
| | - Brigitte F Schmidt
- JGS Research Co., Pittsburgh, Pennsylvania 15212, United States.,Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Nolan M Frey
- Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Sarah M Boothman
- Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Jonathan S Minden
- Impact Proteomics, LLC., Pittsburgh, Pennsylvania 15206, United States.,Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Amber Lucas
- Impact Proteomics, LLC., Pittsburgh, Pennsylvania 15206, United States
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11
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Maitland MER, Kuljanin M, Wang X, Lajoie GA, Schild-Poulter C. Proteomic analysis of ubiquitination substrates reveals a CTLH E3 ligase complex-dependent regulation of glycolysis. FASEB J 2021; 35:e21825. [PMID: 34383978 PMCID: PMC9292413 DOI: 10.1096/fj.202100664r] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 06/25/2021] [Accepted: 07/15/2021] [Indexed: 11/11/2022]
Abstract
Ubiquitination is an essential post‐translational modification that regulates protein stability or function. Its substrate specificity is dictated by various E3 ligases. The human C‐terminal to LisH (CTLH) complex is a newly discovered multi‐subunit really interesting new gene (RING) E3 ligase with only a few known ubiquitination targets. Here, we used mass spectrometry‐based proteomic techniques to gain insight into CTLH complex function and ubiquitination substrates in HeLa cells. First, global proteomics determined proteins that were significantly increased, and thus may be substrates targeted for degradation, in cells depleted of CTLH complex member RanBPM. RanBPM‐dependent ubiquitination determined using diGLY‐enriched proteomics and the endogenous RanBPM interactome further revealed candidate ubiquitination targets. Three glycolysis enzymes alpha‐enolase, L‐lactate dehydrogenase A chain (LDHA), and pyruvate kinase M1/2 (PKM) had decreased ubiquitin sites in shRanBPM cells and were found associated with RanBPM in the interactome. Reduced polyubiquitination was validated for PKM2 and LDHA in cells depleted of RanBPM and CTLH complex RING domain subunit RMND5A. PKM2 and LDHA protein levels were unchanged, yet their activity was increased in extracts of cells with downregulated RanBPM. Finally, RanBPM deficient cells displayed enhanced glycolysis and deregulated central carbon metabolism. Overall, this study identifies potential CTLH complex ubiquitination substrates and uncovers that the CTLH complex inhibits glycolysis via non‐degradative ubiquitination of PKM2 and LDHA.
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Affiliation(s)
- Matthew E R Maitland
- Robarts Research Institute, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada.,Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada.,Don Rix Protein Identification Facility, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | - Miljan Kuljanin
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada.,Don Rix Protein Identification Facility, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | - Xu Wang
- Robarts Research Institute, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | - Gilles A Lajoie
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada.,Don Rix Protein Identification Facility, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | - Caroline Schild-Poulter
- Robarts Research Institute, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada.,Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
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12
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Abstract
Biological mass spectrometry (MS) encompasses a range of methods for characterizing proteins and other biomolecules. MS is uniquely powerful for the structural analysis of endogenous protein complexes, which are often heterogeneous, poorly abundant, and refractive to characterization by other methods. Here, we focus on how biological MS can contribute to the study of endogenous protein complexes, which we define as complexes expressed in the physiological host and purified intact, as opposed to reconstituted complexes assembled from heterologously expressed components. Biological MS can yield information on complex stoichiometry, heterogeneity, topology, stability, activity, modes of regulation, and even structural dynamics. We begin with a review of methods for isolating endogenous complexes. We then describe the various biological MS approaches, focusing on the type of information that each method yields. We end with future directions and challenges for these MS-based methods.
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Affiliation(s)
- Rivkah Rogawski
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Michal Sharon
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
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13
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Aballo TJ, Roberts DS, Melby JA, Buck KM, Brown KA, Ge Y. Ultrafast and Reproducible Proteomics from Small Amounts of Heart Tissue Enabled by Azo and timsTOF Pro. J Proteome Res 2021; 20:4203-4211. [PMID: 34236868 PMCID: PMC8349881 DOI: 10.1021/acs.jproteome.1c00446] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Global bottom-up mass spectrometry (MS)-based proteomics is widely used for protein identification and quantification to achieve a comprehensive understanding of the composition, structure, and function of the proteome. However, traditional sample preparation methods are time-consuming, typically including overnight tryptic digestion, extensive sample cleanup to remove MS-incompatible surfactants, and offline sample fractionation to reduce proteome complexity prior to online liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis. Thus, there is a need for a fast, robust, and reproducible method for protein identification and quantification from complex proteomes. Herein, we developed an ultrafast bottom-up proteomics method enabled by Azo, a photocleavable, MS-compatible surfactant that effectively solubilizes proteins and promotes rapid tryptic digestion, combined with the Bruker timsTOF Pro, which enables deeper proteome coverage through trapped ion mobility spectrometry (TIMS) and parallel accumulation-serial fragmentation (PASEF) of peptides. We applied this method to analyze the complex human cardiac proteome and identified nearly 4000 protein groups from as little as 1 mg of human heart tissue in a single one-dimensional LC-TIMS-MS/MS run with high reproducibility. Overall, we anticipate this ultrafast, robust, and reproducible bottom-up method empowered by both Azo and the timsTOF Pro will be generally applicable and greatly accelerate the throughput of large-scale quantitative proteomic studies. Raw data are available via the MassIVE repository with identifier MSV000087476.
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Affiliation(s)
- Timothy J Aballo
- Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - David S Roberts
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Jake A Melby
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Kevin M Buck
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Kyle A Brown
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department of Surgery, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Ying Ge
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
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14
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Evaluation of Filter, Paramagnetic, and STAGETips Aided Workflows for Proteome Profiling of Symbiodiniaceae Dinoflagellate. Processes (Basel) 2021. [DOI: 10.3390/pr9060983] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The integrity of coral reef ecosystems worldwide rests on a fine-tuned symbiotic interaction between an invertebrate and a dinoflagellate microalga from the family Symbiodiniaceae. Recent advances in bottom-up shotgun proteomic approaches and the availability of vast amounts of genetic information about Symbiodiniaceae have provided a unique opportunity to better understand the molecular mechanisms underpinning the interactions of coral-Symbiodiniaceae. However, the resilience of this dinoflagellate cell wall, as well as the presence of polyanionic and phenolics cell wall components, requires the optimization of sample preparation techniques for successful implementation of bottom-up proteomics. Therefore, in this study we compare three different workflows—filter-aided sample preparation (FASP), single-pot solid-phase-enhanced sample preparation (SP3), and stop-and-go-extraction tips (STAGETips, ST)—to develop a high-throughput proteotyping protocol for Symbiodiniaceae algal research. We used the model isolate Symbiodinium tridacnidorum. We show that SP3 outperformed ST and FASP with regard to robustness, digestion efficiency, and contaminant removal, which led to the highest number of total (3799) and unique proteins detected from 23,593 peptides. Most of these proteins were detected with ≥2 unique peptides (73%), zero missed tryptic peptide cleavages (91%), and hydrophilic peptides (>70%). To demonstrate the functionality of this optimized SP3 sample preparation workflow, we examined the proteome of S. tridacnidorum to better understand the molecular mechanism of peridinin-chlorophyll-protein complex (PCP, light harvesting protein) accumulation under low light (LL, 30 μmol photon m−2 s−1). Cells exposed to LL for 7 days upregulated various light harvesting complex (LHCs) proteins through the mevalonate-independent pathway; proteins of this pathway were at 2- to 6-fold higher levels than the control of 120 μmol photon m−2 s−1. Potentially, LHCs which were maintained in an active phosphorylated state by serine/threonine-protein kinase were also upregulated to 10-fold over control. Collectively, our results show that the SP3 method is an efficient high-throughput proteotyping tool for Symbiodiniaceae algal research.
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15
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Leclerc CJ, Cooper TT, Bell GI, Lajoie GA, Flynn LE, Hess DA. Decellularized adipose tissue scaffolds guide hematopoietic differentiation and stimulate vascular regeneration in a hindlimb ischemia model. Biomaterials 2021; 274:120867. [PMID: 33992837 DOI: 10.1016/j.biomaterials.2021.120867] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Revised: 04/29/2021] [Accepted: 04/29/2021] [Indexed: 12/30/2022]
Abstract
Cellular therapies to stimulate therapeutic angiogenesis in individuals with critical limb ischemia (CLI) remain under intense investigation. In this context, the efficacy of cell therapy is dependent on the survival, biodistribution, and pro-angiogenic paracrine signaling of the cells transplanted. Hematopoietic progenitor cells (HPC) purified from human umbilical cord blood using high aldehyde dehydrogenase-activity (ALDHhi cells) and expanded ex vivo, represent a heterogeneous mixture of progenitor cells previously shown to support limb revascularization in mouse models of CLI. The objectives of this study were to investigate the utility of bioscaffolds derived from human decellularized adipose tissue (DAT) to guide the differentiation of seeded HPC in vitro and harness the pro-angiogenic capacity of HPC at the site of ischemia after implantation in vivo. Probing whether the DAT scaffolds altered HPC differentiation, label-free quantitative mass spectrometry and flow cytometric phenotype analyses indicated that culturing the HPC on the DAT scaffolds supported their differentiation towards the pro-angiogenic monocyte/macrophage lineage at the expense of megakaryopoiesis. Moreover, implantation of HPC in DAT scaffolds within a unilateral hindlimb ischemia model in NOD/SCID mice increased cell retention at the site of ischemia relative to intramuscular injection, and accelerated the recovery of limb perfusion, improved functional limb use and augmented CD31+ capillary density when compared to DAT implantation alone or saline-injected controls. Collectively, these data indicate that cell-instructive DAT scaffolds can direct therapeutic HPC differentiation towards the monocyte/macrophage lineage and represent a promising delivery platform for improving the efficacy of cell therapies for CLI.
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Affiliation(s)
- Christopher J Leclerc
- School of Biomedical Engineering, Amit Chakma Engineering Building, The University of Western Ontario, London, Ontario, Canada, N6A 5B9; Krembil Centre for Stem Cell Biology, Molecular Medicine Research Laboratories, Robarts Research Institute, London, Ontario, N6A 5B6, Canada
| | - Tyler T Cooper
- Krembil Centre for Stem Cell Biology, Molecular Medicine Research Laboratories, Robarts Research Institute, London, Ontario, N6A 5B6, Canada; Don Rix Protein Identification Facility, Department of Biochemistry, University of Western Ontario, London, Ontario, N6G 2V4, Canada
| | - Gillian I Bell
- Krembil Centre for Stem Cell Biology, Molecular Medicine Research Laboratories, Robarts Research Institute, London, Ontario, N6A 5B6, Canada
| | - Gilles A Lajoie
- Don Rix Protein Identification Facility, Department of Biochemistry, University of Western Ontario, London, Ontario, N6G 2V4, Canada
| | - Lauren E Flynn
- School of Biomedical Engineering, Amit Chakma Engineering Building, The University of Western Ontario, London, Ontario, Canada, N6A 5B9; Department of Chemical and Biochemical Engineering, Thompson Engineering Building, The University of Western Ontario, London, Ontario, N6A 5B9, Canada; Department of Anatomy and Cell Biology, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, Ontario, N6A 3K7, Canada
| | - David A Hess
- Krembil Centre for Stem Cell Biology, Molecular Medicine Research Laboratories, Robarts Research Institute, London, Ontario, N6A 5B6, Canada; Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, Ontario, N6A 5C1, Canada.
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16
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Dieters-Castator D, Dantonio PM, Piaseczny M, Zhang G, Liu J, Kuljanin M, Sherman S, Jewer M, Quesnel K, Kang EY, Köbel M, Siegers GM, Leask A, Hess D, Lajoie G, Postovit LM. Embryonic protein NODAL regulates the breast tumor microenvironment by reprogramming cancer-derived secretomes. Neoplasia 2021; 23:375-390. [PMID: 33784590 PMCID: PMC8041663 DOI: 10.1016/j.neo.2021.02.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 02/23/2021] [Accepted: 02/26/2021] [Indexed: 02/07/2023]
Abstract
The tumor microenvironment (TME) is an important mediator of breast cancer progression. Cancer-associated fibroblasts constitute a major component of the TME and may originate from tissue-associated fibroblasts or infiltrating mesenchymal stromal cells (MSCs). The mechanisms by which cancer cells activate fibroblasts and recruit MSCs to the TME are largely unknown, but likely include deposition of a pro-tumorigenic secretome. The secreted embryonic protein NODAL is clinically associated with breast cancer stage and promotes tumor growth, metastasis, and vascularization. Herein, we show that NODAL expression correlates with the presence of activated fibroblasts in human triple-negative breast cancers and that it directly induces Cancer-associated fibroblasts phenotypes. We further show that NODAL reprograms cancer cell secretomes by simultaneously altering levels of chemokines (e.g., CXCL1), cytokines (e.g., IL-6) and growth factors (e.g., PDGFRA), leading to alterations in MSC chemotaxis. We therefore demonstrate a hitherto unappreciated mechanism underlying the dynamic regulation of the TME.
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Affiliation(s)
| | - Paola M Dantonio
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada
| | - Matt Piaseczny
- Department of Anatomy and Cell Biology, Western University, London, ON, Canada
| | - Guihua Zhang
- Department of Oncology, University of Alberta, Edmonton, AB, Canada
| | - Jiahui Liu
- Department of Oncology, University of Alberta, Edmonton, AB, Canada
| | - Miljan Kuljanin
- Robarts Research Institute, London, ON, Canada; Department of Biochemistry, Western University, London, ON, Canada
| | - Stephen Sherman
- Robarts Research Institute, London, ON, Canada; Department of Physiology and Pharmacology, Western University, London, ON, Canada
| | - Michael Jewer
- Department of Anatomy and Cell Biology, Western University, London, ON, Canada; Department of Oncology, University of Alberta, Edmonton, AB, Canada
| | - Katherine Quesnel
- Department of Physiology and Pharmacology, Western University, London, ON, Canada
| | - Eun Young Kang
- Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, AB, Canada
| | - Martin Köbel
- Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, AB, Canada
| | | | - Andrew Leask
- Department of Physiology and Pharmacology, Western University, London, ON, Canada
| | - David Hess
- Robarts Research Institute, London, ON, Canada; Department of Physiology and Pharmacology, Western University, London, ON, Canada
| | - Gilles Lajoie
- Department of Biochemistry, Western University, London, ON, Canada
| | - Lynne-Marie Postovit
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada; Department of Oncology, University of Alberta, Edmonton, AB, Canada.
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17
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Cooper TT, Sherman SE, Bell GI, Dayarathna T, McRae DM, Ma J, Lagugné-Labarthet F, Pasternak SH, Lajoie GA, Hess DA. Ultrafiltration and Injection of Islet Regenerative Stimuli Secreted by Pancreatic Mesenchymal Stromal Cells. Stem Cells Dev 2021; 30:247-264. [PMID: 33403929 PMCID: PMC10331161 DOI: 10.1089/scd.2020.0206] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 01/04/2021] [Indexed: 12/13/2022] Open
Abstract
The secretome of mesenchymal stromal cells (MSCs) is enriched for biotherapeutic effectors contained within and independent of extracellular vesicles (EVs) that may support tissue regeneration as an injectable agent. We have demonstrated that the intrapancreatic injection of concentrated conditioned media (CM) produced by bone marrow MSC supports islet regeneration and restored glycemic control in hyperglycemic mice, ultimately providing a platform to elucidate components of the MSC secretome. Herein, we extend these findings using human pancreas-derived MSC (Panc-MSC) as "biofactories" to enrich for tissue regenerative stimuli housed within distinct compartments of the secretome. Specifically, we utilized 100 kDa ultrafiltration as a simple method to debulk protein mass and to enrich for EVs while concentrating the MSC secretome into an injectable volume for preclinical assessments in murine models of blood vessel and islet regeneration. EV enrichment (EV+) was validated using nanoscale flow cytometry and atomic force microscopy, in addition to the detection of classical EV markers CD9, CD81, and CD63 using label-free mass spectrometry. EV+ CM was predominately enriched with mediators of wound healing and epithelial-to-mesenchymal transition that supported functional regeneration in mesenchymal and nonmesenchymal tissues. For example, EV+ CM supported human microvascular endothelial cell tubule formation in vitro and enhanced the recovery of blood perfusion following intramuscular injection in nonobese diabetic/severe combined immunodeficiency mice with unilateral hind limb ischemia. Furthermore, EV+ CM increased islet number and β cell mass, elevated circulating insulin, and improved glycemic control following intrapancreatic injection in streptozotocin-treated mice. Collectively, this study provides foundational evidence that Panc-MSC, readily propagated from the subculture of human islets, may be utilized for regenerative medicine applications.
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Affiliation(s)
- Tyler T. Cooper
- Department of Physiology and Pharmacology, Western University, London, Canada
- Molecular Medicine Research Laboratories, Robarts Research Institute, London, Canada
- Don Rix Protein Identification Facility, Department of Biochemistry and Western University, London, Canada
| | - Stephen E. Sherman
- Department of Physiology and Pharmacology, Western University, London, Canada
- Molecular Medicine Research Laboratories, Robarts Research Institute, London, Canada
| | - Gillian I. Bell
- Molecular Medicine Research Laboratories, Robarts Research Institute, London, Canada
| | - Thamara Dayarathna
- Molecular Medicine Research Laboratories, Robarts Research Institute, London, Canada
| | | | - Jun Ma
- Molecular Medicine Research Laboratories, Robarts Research Institute, London, Canada
- Don Rix Protein Identification Facility, Department of Biochemistry and Western University, London, Canada
| | | | - Stephen H. Pasternak
- Molecular Medicine Research Laboratories, Robarts Research Institute, London, Canada
| | - Gilles A. Lajoie
- Don Rix Protein Identification Facility, Department of Biochemistry and Western University, London, Canada
| | - David A. Hess
- Department of Physiology and Pharmacology, Western University, London, Canada
- Molecular Medicine Research Laboratories, Robarts Research Institute, London, Canada
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18
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Takemori A, Ishizaki J, Nakashima K, Shibata T, Kato H, Kodera Y, Suzuki T, Hasegawa H, Takemori N. BAC-DROP: Rapid Digestion of Proteome Fractionated via Dissolvable Polyacrylamide Gel Electrophoresis and Its Application to Bottom-Up Proteomics Workflow. J Proteome Res 2020; 20:1535-1543. [PMID: 33356312 DOI: 10.1021/acs.jproteome.0c00749] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The GeLC-MS workflow, which combines low-cost, easy-to-use sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis (SDS-PAGE) with liquid chromatography-mass spectrometry (LC-MS), is very popular in current bottom-up proteomics. However, GeLC-MS requires that PAGE-separated proteins undergo overnight enzymatic digestion in a gel, resulting in more than 20 h of sample preparation for LC-MS. In this study, we overcame the limitations of GeLC-MS by developing a rapid digestion workflow for PAGE separation of proteins using N,N'-bis(acryloyl)cystamine (BAC) cross-linked gels that can be solubilized by reductive treatment. Making use of an established workflow called BAC-DROP (BAC-gel dissolution to digest PAGE-resolved objective proteins), crude proteome samples were fractionated based on molecular weight by BAC cross-linked PAGE. After fractionation, the gel fragments were reductively dissolved in under 5 min, and in-solution trypsin digestion of the protein released from the gel was completed in less than 1 h at 70 °C, equivalent to a 90-95% reduction in time compared to conventional in-gel trypsin digestion. The introduction of the BAC-DROP workflow to the MS assays for inflammatory biomarker CRP and viral marker HBsAg allowed for serum sample preparation to be completed in as little as 5 h, demonstrating successful marker quantification from a 0.5 μL sample of human serum.
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Affiliation(s)
- Ayako Takemori
- Division of Analytical Bio-Medicine, Advanced Research Support Center, Ehime University, Toon 790-8577, Ehime, Japan
| | - Jun Ishizaki
- Department of Hematology, Clinical Immunology and Infectious Diseases, Graduate School of Medicine, Ehime University, Toon 790-8577, Ehime, Japan
| | - Kenji Nakashima
- Department of Virology and Parasitology, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Shizuoka, Japan
| | | | - Hidemasa Kato
- Division of Functional Histology, Department of Functional Biomedicine, Graduate School of Medicine, Ehime University, Toon 790-8577, Ehime, Japan
| | - Yoshio Kodera
- Center for Disease Proteomics, Kitasato University School of Science, Sagamihara 252-0373, Kanagawa, Japan
| | - Tetsuro Suzuki
- Department of Virology and Parasitology, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Shizuoka, Japan
| | - Hitoshi Hasegawa
- Department of Hematology, Clinical Immunology and Infectious Diseases, Graduate School of Medicine, Ehime University, Toon 790-8577, Ehime, Japan
| | - Nobuaki Takemori
- Division of Analytical Bio-Medicine, Advanced Research Support Center, Ehime University, Toon 790-8577, Ehime, Japan
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19
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Sherman SE, Kuljanin M, Cooper TT, Lajoie GA, Hess DA. Purification and Functional Characterization of CD34-Expressing Cell Subsets Following Ex Vivo Expansion of Umbilical Cord Blood-Derived Endothelial Colony-Forming Cells. Stem Cells Dev 2020; 29:895-910. [DOI: 10.1089/scd.2020.0008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Affiliation(s)
- Stephen E. Sherman
- Molecular Medicine Research Group, Krembil Centre for Stem Cell Biology, Robarts Research Institute, London, Ontario, Canada
- Department of Physiology and Pharmacology, Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
| | - Miljan Kuljanin
- Don Rix Protein Identification Facility, Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
| | - Tyler T. Cooper
- Molecular Medicine Research Group, Krembil Centre for Stem Cell Biology, Robarts Research Institute, London, Ontario, Canada
- Department of Physiology and Pharmacology, Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
- Don Rix Protein Identification Facility, Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
| | - Gilles A. Lajoie
- Don Rix Protein Identification Facility, Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
| | - David A. Hess
- Molecular Medicine Research Group, Krembil Centre for Stem Cell Biology, Robarts Research Institute, London, Ontario, Canada
- Department of Physiology and Pharmacology, Department of Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
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20
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A Standardized and Reproducible Proteomics Protocol for Bottom-Up Quantitative Analysis of Protein Samples Using SP3 and Mass Spectrometry. Methods Mol Biol 2019; 1959:65-87. [PMID: 30852816 DOI: 10.1007/978-1-4939-9164-8_5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The broad utility of mass spectrometry (MS) for investigating the proteomes of a diverse array of sample types has significantly expanded the use of this technology in biological studies. This widespread use has resulted in a substantial collection of protocols and acquisition approaches designed to obtain the highest-quality data for each experiment. As a result, distilling this information to develop a standard operating protocol for essential workflows, such as bottom-up quantitative shotgun whole proteome analysis, can be complex for users new to MS technology. Further complicating this matter, in-depth description of the methodological choices is seldom given in the literature. In this work, we describe a workflow for quantitative whole proteome analysis that is suitable for biomarker discovery, giving detailed consideration to important stages, including (1) cell lysis and protein cleanup using SP3 paramagnetic beads, (2) quantitative labeling, (3) offline peptide fractionation, (4) MS analysis, and (5) data analysis and interpretation. Special attention is paid to providing comprehensive details for all stages of this proteomics workflow to enhance transferability to external labs. The standardized protocol described here will provide a simplified resource to the proteomics community toward efficient adaptation of MS technology in proteomics studies.
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21
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The mammalian CTLH complex is an E3 ubiquitin ligase that targets its subunit muskelin for degradation. Sci Rep 2019; 9:9864. [PMID: 31285494 PMCID: PMC6614414 DOI: 10.1038/s41598-019-46279-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 06/17/2019] [Indexed: 12/15/2022] Open
Abstract
The multi-subunit C-terminal to LisH (CTLH) complex is the mammalian homologue of the yeast Gid E3 ubiquitin ligase complex. In this study, we investigated the human CTLH complex and characterized its E3 ligase activity. We confirm that the complex immunoprecipitated from human cells comprises RanBPM, ARMC8 α/β, muskelin, WDR26, GID4 and the RING domain proteins RMND5A and MAEA. We find that loss of expression of individual subunits compromises the stability of other complex members and that MAEA and RMND5A protein levels are interdependent. Using in vitro ubiquitination assays, we demonstrate that the CTLH complex has E3 ligase activity which is dependent on RMND5A and MAEA. We report that the complex can pair with UBE2D1, UBE2D2 and UBE2D3 E2 enzymes and that recombinant RMND5A mediates K48 and K63 poly-ubiquitin chains. Finally, we show a proteasome-dependent increase in the protein levels of CTLH complex member muskelin in RMND5A KO cells. Furthermore, muskelin ubiquitination is dependent on RMND5A, suggesting that it may be a target of the complex. Overall, we further the characterization of the CTLH complex as an E3 ubiquitin ligase complex in human cells and reveal a potential autoregulation mechanism.
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22
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Abstract
A critical step in proteomics analysis is the optimal extraction and processing of protein material to ensure the highest sensitivity in downstream detection. Achieving this requires a sample-handling technology that exhibits unbiased protein manipulation, flexibility in reagent use, and virtually lossless processing. Addressing these needs, the single-pot, solid-phase-enhanced sample-preparation (SP3) technology is a paramagnetic bead-based approach for rapid, robust, and efficient processing of protein samples for proteomic analysis. SP3 uses a hydrophilic interaction mechanism for exchange or removal of components that are commonly used to facilitate cell or tissue lysis, protein solubilization, and enzymatic digestion (e.g., detergents, chaotropes, salts, buffers, acids, and solvents) before downstream proteomic analysis. The SP3 protocol consists of nonselective protein binding and rinsing steps that are enabled through the use of ethanol-driven solvation capture on the surface of hydrophilic beads, and elution of purified material in aqueous conditions. In contrast to alternative approaches, SP3 combines compatibility with a substantial collection of solution additives with virtually lossless and unbiased recovery of proteins independent of input quantity, all in a simplified single-tube protocol. The SP3 protocol is simple and efficient, and can be easily completed by a standard user in ~30 min, including reagent preparation. As a result of these properties, SP3 has successfully been used to facilitate examination of a broad range of sample types spanning simple and complex protein mixtures in large and very small amounts, across numerous organisms. This work describes the steps and extensive considerations involved in performing SP3 in bottom-up proteomics, using a simplified protein cleanup scenario for illustration.
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23
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Kuras M, Betancourt LH, Rezeli M, Rodriguez J, Szasz M, Zhou Q, Miliotis T, Andersson R, Marko-Varga G. Assessing Automated Sample Preparation Technologies for High-Throughput Proteomics of Frozen Well Characterized Tissues from Swedish Biobanks. J Proteome Res 2018; 18:548-556. [PMID: 30462917 DOI: 10.1021/acs.jproteome.8b00792] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Large cohorts of carefully collected clinical tissue materials play a central role in acquiring sufficient depth and statistical power to discover disease-related mechanisms and biomarkers of clinical significance. Manual preparation of such large sample cohorts requires experienced laboratory personnel. This carries other possible downsides such as low throughput, high risk of errors, and low reproducibility. In this work, three automated technologies for high-throughput proteomics of frozen sectioned tissues were compared. The instruments evaluated included the Bioruptor for tissue disruption and protein extraction; the Barocycler, which is able to disrupt tissues and digest the proteins; and the AssayMAP Bravo, a microchromatography platform for protein digestion, peptide desalting, and fractionation. Wide varieties of tissue samples from rat spleen, malignant melanoma, and pancreatic tumors were used for the assessment. The three instruments displayed reproducible and consistent results, as was proven by high correlations and low coefficients of variation between technical replicates and even more importantly, between replicates that were processed in different batches or at different time points. The results from this study allowed us to integrate these technologies into an automated sample preparation workflow for large-scale proteomic studies that are currently ongoing. Data are available via ProteomeXchange with identifiers PXD010296 and PXD011295.
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Affiliation(s)
- Magdalena Kuras
- Division of Clinical Protein Science & Imaging, Department of Clinical Sciences (Lund) and Department of Biomedical Engineering , Lund University , 221 00 Lund , Sweden
| | - Lazaro Hiram Betancourt
- Division of Clinical Protein Science & Imaging, Department of Clinical Sciences (Lund) and Department of Biomedical Engineering , Lund University , 221 00 Lund , Sweden
| | - Melinda Rezeli
- Division of Clinical Protein Science & Imaging, Department of Clinical Sciences (Lund) and Department of Biomedical Engineering , Lund University , 221 00 Lund , Sweden
| | - Jimmy Rodriguez
- Division of Clinical Protein Science & Imaging, Department of Clinical Sciences (Lund) and Department of Biomedical Engineering , Lund University , 221 00 Lund , Sweden
| | - Marcell Szasz
- Department of Pathology , Semmelweis University , Budapest 1085 , Hungary
| | - Qimin Zhou
- Department of Clinical Sciences Lund (Surgery) , Lund University, Lund, Sweden Skane University Hospital , 221 00 Lund , Sweden
| | - Tasso Miliotis
- Division of Clinical Protein Science & Imaging, Department of Clinical Sciences (Lund) and Department of Biomedical Engineering , Lund University , 221 00 Lund , Sweden.,Translational Science, Cardiovascular Renal and Metabolism, IMED Biotech Unit , AstraZeneca , 431 50 Mölndal , Gothenburg , Sweden
| | - Roland Andersson
- Department of Clinical Sciences Lund (Surgery) , Lund University, Lund, Sweden Skane University Hospital , 221 00 Lund , Sweden
| | - Gyorgy Marko-Varga
- Division of Clinical Protein Science & Imaging, Department of Clinical Sciences (Lund) and Department of Biomedical Engineering , Lund University , 221 00 Lund , Sweden.,First Department of Surgery , Tokyo Medical University , 160-8402 Tokyo , Japan
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24
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Yang Y, Anderson E, Zhang S. Evaluation of six sample preparation procedures for qualitative and quantitative proteomics analysis of milk fat globule membrane. Electrophoresis 2018; 39:2332-2339. [PMID: 29644703 PMCID: PMC6146045 DOI: 10.1002/elps.201800042] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 03/28/2018] [Accepted: 03/28/2018] [Indexed: 01/09/2023]
Abstract
Proteomic analysis of membrane proteins is challenged by the proteins solubility and detergent incompatibility with MS analysis. No single perfect protocol can be used to comprehensively characterize the proteome of membrane fraction. Here, we used cow milk fat globule membrane (MFGM) proteome analysis to assess six sample preparation procedures including one in-gel and five in-solution digestion approaches prior to LC-MS/MS analysis. The largest number of MFGM proteins were identified by suspension trapping (S-Trap) and filter-aided sample preparation (FASP) methods, followed by acetone precipitation without clean-up of tryptic peptides method. Protein identifications with highest average coverage was achieved by Chloroform/MeOH, in-gel and S-Trap methods. Most distinct proteins were identified by FASP method, followed by S-Trap. Analyses by Venn diagram, principal-component analysis, hierarchical clustering and the abundance ranking of quantitative proteins highlight differences in the MFGM fraction by the all sample preparation procedures. These results reveal the biased proteins/peptides loss occurred in each protocol. In this study, we found several novel proteins that were not observed previously by in-depth proteomics characterization of MFGM fraction in milk. Thus, a combination of multiple procedures with orthologous properties of sample preparation was demonstrated to improve the protein sequence coverage and expression level accuracy of membrane samples.
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Affiliation(s)
- Yongxin Yang
- Institute of Biotechnology, Cornell University, Ithaca, NY, USA
- Institute of Animal Science and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, P. R. China
| | | | - Sheng Zhang
- Institute of Biotechnology, Cornell University, Ithaca, NY, USA
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25
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Moggridge S, Sorensen PH, Morin GB, Hughes CS. Extending the Compatibility of the SP3 Paramagnetic Bead Processing Approach for Proteomics. J Proteome Res 2018; 17:1730-1740. [PMID: 29565595 DOI: 10.1021/acs.jproteome.7b00913] [Citation(s) in RCA: 156] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The diversity in protein and peptide biochemistry necessitates robust protocols and reagents for efficiently handling and enriching these molecules prior to analysis with mass spectrometry (MS) or other techniques. Further exploration of the paramagnetic bead-based approach, single-pot solid-phase-enhanced sample preparation (SP3), is carried out toward updating and extending previously described conditions and experimental workflows. The SP3 approach was tested in a wide range of experimental scenarios, including (1) binding solvents (acetonitrile, ethanol, isopropanol, acetone), (2) binding pH (acidic vs neutral), (3) solvent/lysate ratios (50-200%, v/v), (4) mixing and rinsing conditions (on-rack vs off-rack rinsing), (5) Enrichment of nondenatured proteins, and (6) capture of individual proteins from noncomplex mixtures. These results highlight the robust handling of proteins in a broad set of scenarios while also enabling the development of a modified SP3 workflow that offers extended compatibility. The modified SP3 approach is used in quantitative in-depth proteome analyses to compare it with commercial paramagnetic bead-based HILIC methods (MagReSyn) and across multiple binding conditions (e.g., pH and solvent during binding). Together, these data reveal the extensive quantitative coverage of the proteome possible with SP3 independent of the binding approach utilized. The results further establish the utility of SP3 for the unbiased handling of peptides and proteins for proteomic applications.
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Affiliation(s)
- Sophie Moggridge
- Canada's Michael Smith Genome Sciences Centre , British Columbia Cancer Agency , Vancouver , British Columbia V5Z 1L3 , Canada.,Department of Biochemistry and Microbiology , University of Victoria , Victoria , British Columbia V8P 3E6 , Canada
| | - Poul H Sorensen
- Department of Molecular Oncology , British Columbia Cancer Research Centre , Vancouver , British Columbia V5Z 1L3 , Canada
| | - Gregg B Morin
- Canada's Michael Smith Genome Sciences Centre , British Columbia Cancer Agency , Vancouver , British Columbia V5Z 1L3 , Canada.,Department of Medical Genetics , University of British Columbia , Vancouver , British Columbia V6H 3N1 , Canada
| | - Christopher S Hughes
- Canada's Michael Smith Genome Sciences Centre , British Columbia Cancer Agency , Vancouver , British Columbia V5Z 1L3 , Canada
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Mata CI, Fabre B, Hertog MLATM, Parsons HT, Deery MJ, Lilley KS, Nicolaï BM. In-depth characterization of the tomato fruit pericarp proteome. Proteomics 2017; 17. [PMID: 27957804 DOI: 10.1002/pmic.201600406] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 11/24/2016] [Accepted: 12/07/2016] [Indexed: 12/19/2022]
Abstract
Since the genome of Solanum lycopersicum L. was published in 2012, some studies have explored its proteome although with a limited depth. In this work, we present an extended characterization of the proteome of the tomato pericarp at its ripe red stage. Fractionation of tryptic peptides generated from pericarp proteins by off-line high-pH reverse-phase phase chromatography in combination with LC-MS/MS analysis on a Fisher Scientific Q Exactive and a Sciex Triple-TOF 6600 resulted in the identification of 8588 proteins with a 1% FDR both at the peptide and protein levels. Proteins were mapped through GO and KEGG databases and a large number of the identified proteins were associated with cytoplasmic organelles and metabolic pathways categories. These results constitute one of the most extensive proteome datasets of tomato so far and provide an experimental confirmation of the existence of a high number of theoretically predicted proteins. All MS data are available in the ProteomeXchange repository with the dataset identifiers PXD004947 and PXD004932.
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Affiliation(s)
| | - Bertrand Fabre
- Cambridge Centre for Proteomics, Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
| | | | - Harriet T Parsons
- Cambridge Centre for Proteomics, Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
| | - Michael J Deery
- Cambridge Centre for Proteomics, Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
| | - Kathryn S Lilley
- Cambridge Centre for Proteomics, Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
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Schmitt ND, Agar JN. Parsing disease-relevant protein modifications from epiphenomena: perspective on the structural basis of SOD1-mediated ALS. JOURNAL OF MASS SPECTROMETRY : JMS 2017; 52:480-491. [PMID: 28558143 PMCID: PMC6002871 DOI: 10.1002/jms.3953] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 05/23/2017] [Accepted: 05/25/2017] [Indexed: 05/08/2023]
Abstract
Conformational change and modification of proteins are involved in many cellular functions. However, they can also have adverse effects that are implicated in numerous diseases. How structural change promotes disease is generally not well-understood. This perspective illustrates how mass spectrometry (MS), followed by toxicological and epidemiological validation, can discover disease-relevant structural changes and therapeutic strategies. We (with our collaborators) set out to characterize the structural and toxic consequences of disease-associated mutations and post-translational modifications (PTMs) of the cytosolic antioxidant protein Cu/Zn-superoxide dismutase (SOD1). Previous genetic studies discovered >180 different mutations in the SOD1 gene that caused familial (inherited) amyotrophic lateral sclerosis (fALS). Using hydrogen-deuterium exchange with mass spectrometry, we determined that diverse disease-associated SOD1 mutations cause a common structural defect - perturbation of the SOD1 electrostatic loop. X-ray crystallographic studies had demonstrated that this leads to protein aggregation through a specific interaction between the electrostatic loop and an exposed beta-barrel edge strand. Using epidemiology methods, we then determined that decreased SOD1 stability and increased protein aggregation are powerful risk factors for fALS progression, with a combined hazard ratio > 300 (for comparison, a lifetime of smoking is associated with a hazard ratio of ~15 for lung cancer). The resulting structural model of fALS etiology supported the hypothesis that some sporadic ALS (sALS, ~80% of ALS is not associated with a gene defect) could be caused by post-translational protein modification of wild-type SOD1. We developed immunocapture antibodies and high sensitivity top-down MS methods and characterized PTMs of wild-type SOD1 using human tissue samples. Using global hydrogen-deuterium exchange, X-ray crystallography and neurotoxicology, we then characterized toxic and protective subsets of SOD1 PTMs. To cap this perspective, we present proof-of-concept that post-translational modification can cause disease. We show that numerous mutations (N➔D; Q➔E), which result in the same chemical structure as the PTM deamidation, cause multiple diseases. Copyright © 2017 John Wiley & Sons, Ltd.
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Affiliation(s)
- Nicholas D. Schmitt
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
- Barnett Institute of Chemical and Biological Analysis, Northeastern University, Boston, MA, USA
| | - Jeffrey N. Agar
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
- Barnett Institute of Chemical and Biological Analysis, Northeastern University, Boston, MA, USA
- Department of Pharmaceutical Sciences, Northeastern University, Boston, MA, USA
- Correspondence Northeastern University, 360 Huntington Avenue, 140 The Fenway, Room 417, Boston, MA 02115
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A Comprehensive Guide for Performing Sample Preparation and Top-Down Protein Analysis. Proteomes 2017; 5:proteomes5020011. [PMID: 28387712 PMCID: PMC5489772 DOI: 10.3390/proteomes5020011] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Revised: 04/04/2017] [Accepted: 04/04/2017] [Indexed: 12/21/2022] Open
Abstract
Methodologies for the global analysis of proteins in a sample, or proteome analysis, have been available since 1975 when Patrick O′Farrell published the first paper describing two-dimensional gel electrophoresis (2D-PAGE). This technique allowed the resolution of single protein isoforms, or proteoforms, into single ‘spots’ in a polyacrylamide gel, allowing the quantitation of changes in a proteoform′s abundance to ascertain changes in an organism′s phenotype when conditions change. In pursuit of the comprehensive profiling of the proteome, significant advances in technology have made the identification and quantitation of intact proteoforms from complex mixtures of proteins more routine, allowing analysis of the proteome from the ‘Top-Down’. However, the number of proteoforms detected by Top-Down methodologies such as 2D-PAGE or mass spectrometry has not significantly increased since O’Farrell’s paper when compared to Bottom-Up, peptide-centric techniques. This article explores and explains the numerous methodologies and technologies available to analyse the proteome from the Top-Down with a strong emphasis on the necessity to analyse intact proteoforms as a better indicator of changes in biology and phenotype. We arrive at the conclusion that the complete and comprehensive profiling of an organism′s proteome is still, at present, beyond our reach but the continuing evolution of protein fractionation techniques and mass spectrometry brings comprehensive Top-Down proteome profiling closer.
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