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Bi B, Qiu M, Liu P, Wang Q, Wen Y, Li Y, Li B, Li Y, He Y, Zhao J. Protein post-translational modifications: A key factor in colorectal cancer resistance mechanisms. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194977. [PMID: 37625568 DOI: 10.1016/j.bbagrm.2023.194977] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 07/16/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023]
Abstract
Colorectal cancer (CRC) is one of the leading causes of cancer-related death. Despite advances in treatment, drug resistance remains a critical impediment. Post-translational modifications (PTMs) regulate protein stability, localization, and activity, impacting vital cellular processes. Recent research has highlighted the essential role of PTMs in the development of CRC resistance. This review summarizes recent advancements in understanding PTMs' roles in CRC resistance, focusing on the latest discoveries. We discuss the functional impact of PTMs on signaling pathways and molecules involved in CRC resistance, progress in drug development, and potential therapeutic targets. We also summarize the primary enrichment methods for PTMs. Finally, we discuss current challenges and future directions, including the need for more comprehensive PTM analysis methods and PTM-targeted therapies. This review identifies potential therapeutic interventions for addressing medication resistance in CRC, proposes prospective therapeutic options, and gives an overview of the function of PTMs in CRC resistance.
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Affiliation(s)
- Bo Bi
- Digestive Diseases Center, The Seventh Affiliated Hospital of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen, Guangdong, China; Guangdong Provincial Key Laboratory of Digestive Cancer Research, The Seventh Affiliated Hospital of Sun Yat-sen University, Sun Yat-Sen University, Shenzhen, Guangdong, China
| | - Miaojuan Qiu
- Digestive Diseases Center, The Seventh Affiliated Hospital of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen, Guangdong, China; Guangdong Provincial Key Laboratory of Digestive Cancer Research, The Seventh Affiliated Hospital of Sun Yat-sen University, Sun Yat-Sen University, Shenzhen, Guangdong, China; Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen, Guangdong, China
| | - Peng Liu
- Digestive Diseases Center, The Seventh Affiliated Hospital of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen, Guangdong, China; Guangdong Provincial Key Laboratory of Digestive Cancer Research, The Seventh Affiliated Hospital of Sun Yat-sen University, Sun Yat-Sen University, Shenzhen, Guangdong, China
| | - Qiang Wang
- Digestive Diseases Center, The Seventh Affiliated Hospital of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen, Guangdong, China; Guangdong Provincial Key Laboratory of Digestive Cancer Research, The Seventh Affiliated Hospital of Sun Yat-sen University, Sun Yat-Sen University, Shenzhen, Guangdong, China
| | - Yingfei Wen
- Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen, Guangdong, China
| | - You Li
- Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen, Guangdong, China
| | - Binbin Li
- Digestive Diseases Center, The Seventh Affiliated Hospital of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen, Guangdong, China; Guangdong Provincial Key Laboratory of Digestive Cancer Research, The Seventh Affiliated Hospital of Sun Yat-sen University, Sun Yat-Sen University, Shenzhen, Guangdong, China; Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen, Guangdong, China
| | - Yongshu Li
- Hubei Normal University, College of Life Sciences Huangshi, Hubei, China.
| | - Yulong He
- Digestive Diseases Center, The Seventh Affiliated Hospital of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen, Guangdong, China; Guangdong Provincial Key Laboratory of Digestive Cancer Research, The Seventh Affiliated Hospital of Sun Yat-sen University, Sun Yat-Sen University, Shenzhen, Guangdong, China.
| | - Jing Zhao
- Digestive Diseases Center, The Seventh Affiliated Hospital of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen, Guangdong, China; Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen, Guangdong, China.
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Mithoe SC, Menke FLH. Titanium Oxide-Based Phosphopeptide Enrichment from Arabidopsis Seedlings. Methods Mol Biol 2023; 2581:255-265. [PMID: 36413323 DOI: 10.1007/978-1-0716-2784-6_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Protein phosphorylation is one of the most widely studied posttranslational modifications, and its role in signal transduction has gained particular attention. The relatively low abundance of the phosphorylated form of proteins makes identification by mass spectrometry challenging in the absence of selective enrichment. Titanium oxide-based enrichment of phosphopeptides in the presence of acidic modifiers is highly selective and makes it technically possible to detect thousands of phosphopeptides in a single sample by liquid chromatography-mass spectrometry. In this chapter, we describe a detailed protocol for the selective enrichment of microsomal and cytosolic phosphopeptides from Arabidopsis seedlings. The resulting phosphopeptide fractions enable routine identification of several thousands of phosphopeptide spectra per sample by mass spectrometry.
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Affiliation(s)
| | - Frank L H Menke
- The Sainsbury Laboratory, Norwich Research Park, University of East Anglia, Norwich, UK.
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Zeng X, Lan Y, Xiao J, Hu L, Tan L, Liang M, Wang X, Lu S, Peng T, Long F. Advances in phosphoproteomics and its application to COPD. Expert Rev Proteomics 2022; 19:311-324. [PMID: 36730079 DOI: 10.1080/14789450.2023.2176756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
INTRODUCTION Chronic obstructive pulmonary disease (COPD) was the third leading cause of global death in 2019, causing a huge economic burden to society. Therefore, it is urgent to identify specific phenotypes of COPD patients through early detection, and to promptly treat exacerbations. The field of phosphoproteomics has been a massive advancement, compelled by the developments in mass spectrometry, enrichment strategies, algorithms, and tools. Modern mass spectrometry-based phosphoproteomics allows understanding of disease pathobiology, biomarker discovery, and predicting new therapeutic modalities. AREAS COVERED In this article, we present an overview of phosphoproteomic research and strategies for enrichment and fractionation of phosphopeptides, identification of phosphorylation sites, chromatographic separation and mass spectrometry detection strategies, and the potential application of phosphorylated proteomic analysis in the diagnosis, treatment, and prognosis of COPD disease. EXPERT OPINION The role of phosphoproteomics in COPD is critical for understanding disease pathobiology, identifying potential biomarkers, and predicting new therapeutic approaches. However, the complexity of COPD requires the more comprehensive understanding that can be achieved through integrated multi-omics studies. Phosphoproteomics, as a part of these multi-omics approaches, can provide valuable insights into the underlying mechanisms of COPD.
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Affiliation(s)
- Xiaoyin Zeng
- Sino-French Hoffmann Institute, School of Basic Medical Science, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
| | - Yanting Lan
- Sino-French Hoffmann Institute, School of Basic Medical Science, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
| | - Jing Xiao
- Sino-French Hoffmann Institute, School of Basic Medical Science, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
| | - Longbo Hu
- Sino-French Hoffmann Institute, School of Basic Medical Science, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
| | - Long Tan
- Sino-French Hoffmann Institute, School of Basic Medical Science, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
| | - Mengdi Liang
- Sino-French Hoffmann Institute, School of Basic Medical Science, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
| | - Xufei Wang
- Sino-French Hoffmann Institute, School of Basic Medical Science, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
| | - Shaohua Lu
- Sino-French Hoffmann Institute, School of Basic Medical Science, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
| | - Tao Peng
- Sino-French Hoffmann Institute, School of Basic Medical Science, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, China.,Guangdong South China Vaccine Co. Ltd, Guangzhou, China
| | - Fei Long
- Sino-French Hoffmann Institute, School of Basic Medical Science, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
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Zhu G, Jin L, Sun W, Wang S, Liu N. Proteomics of post-translational modifications in colorectal cancer: Discovery of new biomarkers. Biochim Biophys Acta Rev Cancer 2022; 1877:188735. [PMID: 35577141 DOI: 10.1016/j.bbcan.2022.188735] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 05/08/2022] [Accepted: 05/09/2022] [Indexed: 02/07/2023]
Abstract
Colorectal cancer (CRC) is one of the costliest health problems and ranks second in cancer-related mortality in developed countries. With the aid of proteomics, many protein biomarkers for the diagnosis, prognosis, and precise management of CRC have been identified. Furthermore, some protein biomarkers exhibit structural diversity after modifications. Post-translational modifications (PTMs), most of which are catalyzed by a variety of enzymes, extensively increase protein diversity and are involved in many complex and dynamic cellular processes through the regulation of protein function. Accumulating evidence suggests that abnormal PTM events are associated with a variety of human diseases, such as CRC, thus highlighting the need for studying PTMs to discover both the molecular mechanisms and therapeutic targets of CRC. In this review, we begin with a brief overview of the importance of protein PTMs, discuss the general strategies for proteomic profiling of several key PTMs (including phosphorylation, acetylation, glycosylation, ubiquitination, methylation, and citrullination), shift the emphasis to describing the specific methods used for delineating the global landscapes of each of these PTMs, and summarize the recent applications of these methods to explore the potential roles of the PTMs in CRC. Finally, we discuss the current status of PTM research on CRC and provide future perspectives on how PTM regulation can play an essential role in translational medicine for early diagnosis, prognosis stratification, and therapeutic intervention in CRC.
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Affiliation(s)
- Gengjun Zhu
- Department Oncology and Hematology, The Second Hospital of Jilin University, Changchun, China
| | - Lifang Jin
- Department Oncology and Hematology, The Second Hospital of Jilin University, Changchun, China
| | - Wanchun Sun
- Key Laboratory of Zoonosis Research, Ministry of Education, Jilin University, Changchun, China
| | - Shuang Wang
- Dermatological department, The Second Hospital of Jilin University, Changchun, China.
| | - Ning Liu
- Key Laboratory of Zoonosis Research, Ministry of Education, Jilin University, Changchun, China; Central Laboratory, The Second Hospital of Jilin University, Changchun, China.
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Colomé N, Abian J, Aloria K, Arizmendi JM, Barceló-Batllori S, Braga-Lagache S, Burlet-Schiltz O, Carrascal M, Casal JI, Chicano-Gálvez E, Chiva C, Clemente LF, Elortza F, Estanyol JM, Fernandez-Irigoyen J, Fernández-Puente P, Fidalgo MJ, Froment C, Fuentes M, Fuentes-Almagro C, Gay M, Hainard A, Heller M, Hernández ML, Ibarrola N, Iloro I, Kieselbach T, Lario A, Locard-Paulet M, Marina-Ramírez A, Martín L, Morato-López E, Muñoz J, Navajas R, Odena MA, Odriozola L, de Oliveira E, Paradela A, Pasquarello C, de Los Rios V, Ruiz-Romero C, Sabidó E, Sánchez Del Pino M, Sancho J, Santamaría E, Schaeffer-Reiss C, Schneider J, de la Torre C, Valero ML, Vilaseca M, Wu S, Wu L, Ximénez de Embún P, Canals F, Corrales FJ. Multi-laboratory experiment PME11 for the standardization of phosphoproteome analysis. J Proteomics 2022; 251:104409. [PMID: 34758407 DOI: 10.1016/j.jprot.2021.104409] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 10/12/2021] [Accepted: 10/27/2021] [Indexed: 11/16/2022]
Abstract
Global analysis of protein phosphorylation by mass spectrometry proteomic techniques has emerged in the last decades as a powerful tool in biological and biomedical research. However, there are several factors that make the global study of the phosphoproteome more challenging than measuring non-modified proteins. The low stoichiometry of the phosphorylated species and the need to retrieve residue specific information require particular attention on sample preparation, data acquisition and processing to ensure reproducibility, qualitative and quantitative robustness and ample phosphoproteome coverage in phosphoproteomic workflows. Aiming to investigate the effect of different variables in the performance of proteome wide phosphoprotein analysis protocols, ProteoRed-ISCIII and EuPA launched the Proteomics Multicentric Experiment 11 (PME11). A reference sample consisting of a yeast protein extract spiked in with different amounts of a phosphomix standard (Sigma/Merck) was distributed to 31 laboratories around the globe. Thirty-six datasets from 23 laboratories were analyzed. Our results indicate the suitability of the PME11 reference sample to benchmark and optimize phosphoproteomics strategies, weighing the influence of different factors, as well as to rank intra and inter laboratory performance.
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Affiliation(s)
- Núria Colomé
- ProteoRed-ISCIII, Vall d'Hebron Institute of Oncology (VHIO), Barcelona 08035, Spain
| | - Joaquín Abian
- ProteoRed-ISCIII, Instituto de Investigaciones Biomédicas de Barcelona, IIBB-CSIC/IDIBAPS, 08036 Barcelona, Spain
| | - Kerman Aloria
- ProteoRed-ISCIII, Proteomics Core Facility-SGIKER, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Jesús M Arizmendi
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | | | - Sophie Braga-Lagache
- Department for BioMedical Research (DBMR), Proteomics and Mass Spectrometry Core Facility, University of Bern, CH-3010 Bern, Switzerland
| | - Odile Burlet-Schiltz
- Proteomics and Mass Spectrometry of Biomolecules, Proteomics Infrastructure of Toulouse, Proteomics French Infrastructure, ProFI. Institut de Pharmacologie et Biologie Structurale (IPBS), Université de Toulouse, UPS, CNRS, Toulouse, France
| | - Montse Carrascal
- ProteoRed-ISCIII, Instituto de Investigaciones Biomédicas de Barcelona, IIBB-CSIC/IDIBAPS, 08036 Barcelona, Spain
| | - J Ignacio Casal
- ProteoRed-ISCIII, Centro de Investigaciones Biológicas-CSIC, Madrid 28040, Spain
| | - Eduard Chicano-Gálvez
- ProteoRed-ISCIII, Proteomics Unit, IMIBIC/UCO/HURS, IMIBIC Building Fl.3, 14004 Córdoba, Spain
| | - Cristina Chiva
- Proteomics Unit, Center for Genomics Regulation, Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; ProteoRed ISCIII, Proteomics Unit, Universitat Pompeu Fabra, Barcelona, Spain
| | | | - Felix Elortza
- ProteoRed-ISCIII, CIC bioGUNE, Proteomics Platform, Basque Research & Technology Alliance (BRTA), CIBERehd,Bizkaia Science and Technology Park, 48160 Derio, Spain
| | - Josep M Estanyol
- ProteoRed-ISCIII, Scientific and Technological Centers (CCiTUB), University of Barcelona, 08036 Barcelona, Spain
| | - Joaquín Fernandez-Irigoyen
- Proteored-ISCIII. Proteomics Unit, Clinical Neuroproteomics Group, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, 31008 Pamplona, Spain
| | - Patricia Fernández-Puente
- Grupo de Investigación de Reumatología (GIR), Agrupación CICA-INIBIC, Universidad de A Coruña, A Coruña, Spain
| | - María José Fidalgo
- ProteoRed-ISCIII, Scientific and Technological Centers (CCiTUB), University of Barcelona, 08036 Barcelona, Spain
| | - Carine Froment
- Proteomics and Mass Spectrometry of Biomolecules, Proteomics Infrastructure of Toulouse, Proteomics French Infrastructure, ProFI. Institut de Pharmacologie et Biologie Structurale (IPBS), Université de Toulouse, UPS, CNRS, Toulouse, France
| | - Manuel Fuentes
- Department of Medicine and General Cytometry Service-Nucleus, Proteomics Unit, CIBERONC, Cancer Research Center (IBMCC/CSIC/USAL/IBSAL), Universidad de Salamanca, Spain
| | - Carlos Fuentes-Almagro
- Proteomics Unit, SCAI, University of Córdoba, Ramón y Cajal Building, Rabanales Campus, 14071, Córdoba, Spain
| | - Marina Gay
- ProteoRed-ISCIII, Institute for Research in Biomedicine (IRB Barcelona), BIST (The Barcelona Institute of Science and Technology), Baldiri i Reixac 10, 08028 Barcelona, Spain
| | | | - Manfred Heller
- Department for BioMedical Research (DBMR), Proteomics and Mass Spectrometry Core Facility, University of Bern, CH-3010 Bern, Switzerland
| | | | - Nieves Ibarrola
- ProteoRed-ISCIII, Proteomics Unit. Cancer Research Center (IBMCC/CSIC/USAL/IBSAL), Universidad de Salamanca-CSIC, Salamanca, Spain
| | - Ibon Iloro
- ProteoRed-ISCIII, CIC bioGUNE, Proteomics Platform, Basque Research & Technology Alliance (BRTA), CIBERehd,Bizkaia Science and Technology Park, 48160 Derio, Spain
| | | | | | - Marie Locard-Paulet
- Proteomics and Mass Spectrometry of Biomolecules, Proteomics Infrastructure of Toulouse, Proteomics French Infrastructure, ProFI. Institut de Pharmacologie et Biologie Structurale (IPBS), Université de Toulouse, UPS, CNRS, Toulouse, France
| | | | - Luna Martín
- ProteoRed-ISCIII, Vall d'Hebron Institute of Oncology (VHIO), Barcelona 08035, Spain
| | | | - Javier Muñoz
- ProteoRed-ISCIII, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain
| | - Rosana Navajas
- ProteoRed-ISCIII, Centro Nacional de Biotecnologia (CSIC), 28049, Madrid, Spain
| | - M Antonia Odena
- ProteoRed-ISCIII, Proteomics Platform, Barcelona Science Park, 08028, Barcelona, Spain
| | - Leticia Odriozola
- ProteoRed-ISCIII, CIMA, University of Navarra, 31008, Pamplona, Spain
| | - Eliandre de Oliveira
- ProteoRed-ISCIII, Proteomics Platform, Barcelona Science Park, 08028, Barcelona, Spain
| | - Alberto Paradela
- ProteoRed-ISCIII, Centro Nacional de Biotecnologia (CSIC), 28049, Madrid, Spain
| | | | - Vivian de Los Rios
- ProteoRed-ISCIII, Centro de Investigaciones Biológicas-CSIC, Madrid 28040, Spain
| | - Cristina Ruiz-Romero
- Grupo de Investigación de Reumatología (GIR) - ProteoRed-ISCIII, Unidad de Proteómica, INIBIC-Complejo Hospitalario Universitario de A Coruña, SERGAS, A Coruña, Spain
| | - Eduard Sabidó
- Proteomics Unit, Center for Genomics Regulation, Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; ProteoRed ISCIII, Proteomics Unit, Universitat Pompeu Fabra, Barcelona, Spain
| | - Manuel Sánchez Del Pino
- Biotechnology and Biomedicine Interdisciplinary Research Unit (ERI BIOTECMED), University of Valencia, 46100 Burjassot, Spain
| | - Jaime Sancho
- ProteoRed-ISCIII, IPBLN -CSIC, 18016 Granada, Spain
| | - Enrique Santamaría
- Proteored-ISCIII. Proteomics Unit, Clinical Neuroproteomics Group, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, 31008 Pamplona, Spain
| | - Christine Schaeffer-Reiss
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, 67000, Strasbourg, France
| | - Justine Schneider
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, 67000, Strasbourg, France
| | - Carolina de la Torre
- ProteoRed-ISCIII, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
| | - M Luz Valero
- ProteoRed-ISCIII, Proteomics Unit, Central Service for Experimental Research (SCSIE), University of Valencia, 46100, Burjassot, Spain
| | - Marta Vilaseca
- ProteoRed-ISCIII, Institute for Research in Biomedicine (IRB Barcelona), BIST (The Barcelona Institute of Science and Technology), Baldiri i Reixac 10, 08028 Barcelona, Spain
| | - Shuai Wu
- Agilent Technologies, Inc., Santa Clara, CA 95051, USA
| | - Linfeng Wu
- Agilent Technologies, Inc., Santa Clara, CA 95051, USA
| | | | - Francesc Canals
- ProteoRed-ISCIII, Vall d'Hebron Institute of Oncology (VHIO), Barcelona 08035, Spain.
| | - Fernando J Corrales
- ProteoRed-ISCIII, Centro Nacional de Biotecnologia (CSIC), 28049, Madrid, Spain; ProteoRed-ISCIII, CIMA, University of Navarra, 31008, Pamplona, Spain.
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- ProteoRed-ISCIII, Centro Nacional de Biotecnologia (CSIC), 28049, Madrid, Spain; ProteoRed-ISCIII-PRB3, Spanish Proteomics Networked Platform, Centro Nacional de Biotecnología (CSIC), 28049, Madrid, Spain
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- ProteoRed-ISCIII, Centro Nacional de Biotecnologia (CSIC), 28049, Madrid, Spain; European Proteomics Association, Standardization Initiative, , Centro Nacional de Biotecnología (CSIC), 28049, Madrid, Spain
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Liu X, Fields R, Schweppe DK, Paulo JA. Strategies for mass spectrometry-based phosphoproteomics using isobaric tagging. Expert Rev Proteomics 2021; 18:795-807. [PMID: 34652972 DOI: 10.1080/14789450.2021.1994390] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
INTRODUCTION Protein phosphorylation is a primary mechanism of signal transduction in cellular systems. Isobaric tagging can be used to investigate alterations in phosphorylation events in sample multiplexing experiments where quantification extends across all conditions. As such, innovations in tandem mass tag methods can facilitate the expansion of the depth and breadth of phosphoproteomic analyses. AREAS COVERED This review discusses the current state of tandem mass tag-centric phosphoproteomics and highlights advances in reagent chemistry, instrumentation, data acquisition, and data analysis. We stress that approaches for phosphoproteomic investigations require high-specificity enrichment, sensitive detection, and accurate phosphorylation site localization. EXPERT OPINION Tandem mass tag-centric phosphoproteomics will continue to be an important conduit for our understanding of signal transduction in living organisms. We anticipate that progress in phosphopeptide enrichment methodologies, enhancements in instrumentation and data acquisition technologies, and further refinements in analytical strategies will be key to the discovery of biologically relevant findings from phosphoproteomics studies.
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Affiliation(s)
- Xinyue Liu
- Department of Cell Biology, Harvard Medical School, Boston, USA
| | - Rose Fields
- Department of Genome Sciences, University of Washington, Seattle, USA
| | - Devin K Schweppe
- Department of Genome Sciences, University of Washington, Seattle, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, USA
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Nalbantoglu S, Karadag A. Metabolomics bridging proteomics along metabolites/oncometabolites and protein modifications: Paving the way toward integrative multiomics. J Pharm Biomed Anal 2021; 199:114031. [PMID: 33857836 DOI: 10.1016/j.jpba.2021.114031] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 03/02/2021] [Accepted: 03/16/2021] [Indexed: 02/08/2023]
Abstract
Systems biology adopted functional and integrative multiomics approaches enable to discover the whole set of interacting regulatory components such as genes, transcripts, proteins, metabolites, and metabolite dependent protein modifications. This interactome build up the midpoint of protein-protein/PTM, protein-DNA/RNA, and protein-metabolite network in a cell. As the key drivers in cellular metabolism, metabolites are precursors and regulators of protein post-translational modifications [PTMs] that affect protein diversity and functionality. The precisely orchestrated core pattern of metabolic networks refer to paradigm 'metabolites regulate PTMs, PTMs regulate enzymes, and enzymes modulate metabolites' through a multitude of feedback and feed-forward pathway loops. The concept represents a flawless PTM-metabolite-enzyme(protein) regulomics underlined in reprogramming cancer metabolism. Immense interconnectivity of those biomolecules in their spectacular network of intertwined metabolic pathways makes integrated proteomics and metabolomics an excellent opportunity, and the central component of integrative multiomics framework. It will therefore be of significant interest to integrate global proteome and PTM-based proteomics with metabolomics to achieve disease related altered levels of those molecules. Thereby, present update aims to highlight role and analysis of interacting metabolites/oncometabolites, and metabolite-regulated PTMs loop which may function as translational monitoring biomarkers along the reprogramming continuum of oncometabolism.
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Affiliation(s)
- Sinem Nalbantoglu
- TUBITAK Marmara Research Center, Gene Engineering and Biotechnology Institute, Molecular, Oncology Laboratory, Gebze, Kocaeli, Turkey.
| | - Abdullah Karadag
- TUBITAK Marmara Research Center, Gene Engineering and Biotechnology Institute, Molecular, Oncology Laboratory, Gebze, Kocaeli, Turkey
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Label-Free Quantitative Phosphoproteomics of the Fission Yeast Schizosaccharomyces pombe Using Strong Anion Exchange- and Porous Graphitic Carbon-Based Fractionation Strategies. Int J Mol Sci 2021; 22:ijms22041747. [PMID: 33572424 PMCID: PMC7916215 DOI: 10.3390/ijms22041747] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/03/2021] [Accepted: 02/05/2021] [Indexed: 12/26/2022] Open
Abstract
The phosphorylation of proteins modulates various functions of proteins and plays an important role in the regulation of cell signaling. In recent years, label-free quantitative (LFQ) phosphoproteomics has become a powerful tool to analyze the phosphorylation of proteins within complex samples. Despite the great progress, the studies of protein phosphorylation are still limited in throughput, robustness, and reproducibility, hampering analyses that involve multiple perturbations, such as those needed to follow the dynamics of phosphoproteomes. To address these challenges, we introduce here the LFQ phosphoproteomics workflow that is based on Fe-IMAC phosphopeptide enrichment followed by strong anion exchange (SAX) and porous graphitic carbon (PGC) fractionation strategies. We applied this workflow to analyze the whole-cell phosphoproteome of the fission yeast Schizosaccharomyces pombe. Using this strategy, we identified 8353 phosphosites from which 1274 were newly identified. This provides a significant addition to the S. pombe phosphoproteome. The results of our study highlight that combining of PGC and SAX fractionation strategies substantially increases the robustness and specificity of LFQ phosphoproteomics. Overall, the presented LFQ phosphoproteomics workflow opens the door for studies that would get better insight into the complexity of the protein kinase functions of the fission yeast S. pombe.
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Mattè A, Federti E, Tibaldi E, Di Paolo ML, Bisello G, Bertoldi M, Carpentieri A, Pucci P, Iatcencko I, Wilson AB, Riccardi V, Siciliano A, Turrini F, Kim DW, Choi SY, Brunati AM, De Franceschi L. Tyrosine Phosphorylation Modulates Peroxiredoxin-2 Activity in Normal and Diseased Red Cells. Antioxidants (Basel) 2021; 10:antiox10020206. [PMID: 33535382 PMCID: PMC7912311 DOI: 10.3390/antiox10020206] [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: 11/29/2020] [Revised: 01/20/2021] [Accepted: 01/21/2021] [Indexed: 11/16/2022] Open
Abstract
Peroxiredoxin-2 (Prx2) is the third most abundant cytoplasmic protein in red blood cells. Prx2 belongs to a well-known family of antioxidants, the peroxiredoxins (Prxs), that are widely expressed in mammalian cells. Prx2 is a typical, homodimeric, 2-Cys Prx that uses two cysteine residues to accomplish the task of detoxifying a vast range of organic peroxides, H2O2, and peroxynitrite. Although progress has been made on functional characterization of Prx2, much still remains to be investigated on Prx2 post-translational changes. Here, we first show that Prx2 is Tyrosine (Tyr) phosphorylated by Syk in red cells exposed to oxidation induced by diamide. We identified Tyr-193 in both recombinant Prx2 and native Prx2 from red cells as a specific target of Syk. Bioinformatic analysis suggests that phosphorylation of Tyr-193 allows Prx2 conformational change that is more favorable for its peroxidase activity. Indeed, Syk-induced Tyr phosphorylation of Prx2 enhances in vitro Prx2 activity, but also contributes to Prx2 translocation to the membrane of red cells exposed to diamide. The biologic importance of Tyr-193 phospho-Prx2 is further supported by data on red cells from a mouse model of humanized sickle cell disease (SCD). SCD is globally distributed, hereditary red cell disorder, characterized by severe red cell oxidation due to the pathologic sickle hemoglobin. SCD red cells show Tyr-phosphorylated Prx2 bound to the membrane and increased Prx2 activity when compared to healthy erythrocytes. Collectively, our data highlight the novel link between redox related signaling and Prx2 function in normal and diseased red cells.
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Affiliation(s)
- Alessandro Mattè
- Department of Medicine, University of Verona and AOUI Verona, 37134 Verona, Italy; (A.M.); (E.F.); (I.I.); (A.B.W.); (V.R.); (A.S.)
| | - Enrica Federti
- Department of Medicine, University of Verona and AOUI Verona, 37134 Verona, Italy; (A.M.); (E.F.); (I.I.); (A.B.W.); (V.R.); (A.S.)
| | - Elena Tibaldi
- Department of Molecular Medicine, University of Padua, 35128 Padua, Italy; (E.T.); (M.L.D.P.); (A.M.B.)
| | - Maria Luisa Di Paolo
- Department of Molecular Medicine, University of Padua, 35128 Padua, Italy; (E.T.); (M.L.D.P.); (A.M.B.)
| | - Giovanni Bisello
- Department of Neuroscience, Biomedicine and Movement Sciences, Section of Biological Chemistry, University of Verona, 37134 Verona, Italy;
| | - Mariarita Bertoldi
- Department of Neuroscience, Biomedicine and Movement Sciences, Section of Biological Chemistry, University of Verona, 37134 Verona, Italy;
- Correspondence: (M.B.); (L.D.F.); Tel.: +39-045-8027671 (M.B.); +39-045-8124401 (L.D.F.)
| | - Andrea Carpentieri
- Department of Chemical Sciences, University Federico II of Napoli, 80126 Napoli, Italy; (A.C.); (P.P.)
| | - Pietro Pucci
- Department of Chemical Sciences, University Federico II of Napoli, 80126 Napoli, Italy; (A.C.); (P.P.)
- CEINGE Biotecnologie Avanzate, 80145 Napoli, Italy
| | - Iana Iatcencko
- Department of Medicine, University of Verona and AOUI Verona, 37134 Verona, Italy; (A.M.); (E.F.); (I.I.); (A.B.W.); (V.R.); (A.S.)
| | - Anand B. Wilson
- Department of Medicine, University of Verona and AOUI Verona, 37134 Verona, Italy; (A.M.); (E.F.); (I.I.); (A.B.W.); (V.R.); (A.S.)
| | - Veronica Riccardi
- Department of Medicine, University of Verona and AOUI Verona, 37134 Verona, Italy; (A.M.); (E.F.); (I.I.); (A.B.W.); (V.R.); (A.S.)
| | - Angela Siciliano
- Department of Medicine, University of Verona and AOUI Verona, 37134 Verona, Italy; (A.M.); (E.F.); (I.I.); (A.B.W.); (V.R.); (A.S.)
| | | | - Dae Won Kim
- Department of Biomedical Sciences and Institute of Bioscience and Biotechnology, Hallym University, Chuncheon 24252, Korea; (D.W.K.); (S.Y.C.)
| | - Soo Young Choi
- Department of Biomedical Sciences and Institute of Bioscience and Biotechnology, Hallym University, Chuncheon 24252, Korea; (D.W.K.); (S.Y.C.)
| | - Anna Maria Brunati
- Department of Molecular Medicine, University of Padua, 35128 Padua, Italy; (E.T.); (M.L.D.P.); (A.M.B.)
| | - Lucia De Franceschi
- Department of Medicine, University of Verona and AOUI Verona, 37134 Verona, Italy; (A.M.); (E.F.); (I.I.); (A.B.W.); (V.R.); (A.S.)
- Correspondence: (M.B.); (L.D.F.); Tel.: +39-045-8027671 (M.B.); +39-045-8124401 (L.D.F.)
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Thingholm TE, Rönnstrand L, Rosenberg PA. Why and how to investigate the role of protein phosphorylation in ZIP and ZnT zinc transporter activity and regulation. Cell Mol Life Sci 2020; 77:3085-3102. [PMID: 32076742 PMCID: PMC7391401 DOI: 10.1007/s00018-020-03473-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 01/13/2020] [Accepted: 01/28/2020] [Indexed: 12/20/2022]
Abstract
Zinc is required for the regulation of proliferation, metabolism, and cell signaling. It is an intracellular second messenger, and the cellular level of ionic, mobile zinc is strictly controlled by zinc transporters. In mammals, zinc homeostasis is primarily regulated by ZIP and ZnT zinc transporters. The importance of these transporters is underscored by the list of diseases resulting from changes in transporter expression and activity. However, despite numerous structural studies of the transporters revealing both zinc binding sites and motifs important for transporter function, the exact molecular mechanisms regulating ZIP and ZnT activities are still not clear. For example, protein phosphorylation was found to regulate ZIP7 activity resulting in the release of Zn2+ from intracellular stores leading to phosphorylation of tyrosine kinases and activation of signaling pathways. In addition, sequence analyses predict all 24 human zinc transporters to be phosphorylated suggesting that protein phosphorylation is important for regulation of transporter function. This review describes how zinc transporters are implicated in a number of important human diseases. It summarizes the current knowledge regarding ZIP and ZnT transporter structures and points to how protein phosphorylation seems to be important for the regulation of zinc transporter activity. The review addresses the need to investigate the role of protein phosphorylation in zinc transporter function and regulation, and argues for a pressing need to introduce quantitative phosphoproteomics to specifically target zinc transporters and proteins involved in zinc signaling. Finally, different quantitative phosphoproteomic strategies are suggested.
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Affiliation(s)
- T E Thingholm
- Department of Molecular Medicine, Cancer and Inflammation Research, University of Southern Denmark, J.B. Winsløws Vej 25, 3, 5000, Odense C, Denmark.
| | - L Rönnstrand
- Division of Translational Cancer Research, Lund University, Medicon Village, Building 404, Scheelevägen 2, Lund, Sweden
- Lund Stem Cell Center, Lund University, Medicon Village, Building 404, Scheelevägen 2, Lund, Sweden
- Division of Oncology, Skåne University Hospital, Lund, Sweden
| | - P A Rosenberg
- Department of Neurology and F.M. Kirby Neurobiology Center, Boston Children's Hospital, 300 Longwood Ave, Boston, MA, 02115, USA
- Department of Neurology and Program in Neuroscience, Harvard Medical School, Boston, MA, 02115, USA
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11
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Qiu W, Evans CA, Landels A, Pham TK, Wright PC. Phosphopeptide enrichment for phosphoproteomic analysis - A tutorial and review of novel materials. Anal Chim Acta 2020; 1129:158-180. [PMID: 32891386 DOI: 10.1016/j.aca.2020.04.053] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 04/23/2020] [Accepted: 04/24/2020] [Indexed: 12/12/2022]
Abstract
Significant technical advancements in phosphopeptide enrichment have enabled the identification of thousands of p-peptides (mono and multiply phosphorylated) in a single experiment. However, it is still not possible to enrich all p-peptide species in a single step. A range of new techniques and materials has been developed, with the potential to provide a step-change in phosphopeptide enrichment. The first half of this review contains a tutorial for new potential phosphoproteomic researchers; discussing the key steps of a typical phosphoproteomic experiment used to investigate canonical phosphorylation sites (serine, threonine and tyrosine). The latter half then show-cases the latest developments in p-peptide enrichment including: i) Strategies to mitigate non-specific binding in immobilized metal ion affinity chromatography and metal oxide affinity chromatography protocols; ii) Techniques to separate multiply phosphorylated peptides from monophosphorylated peptides (including canonical from non-canonical phosphorylated peptides), or to simultaneously co-enrich other post-translational modifications; iii) New hybrid materials and methods directed towards enhanced selectivity and efficiency of metal-based enrichment; iv) Novel materials that hold promise for enhanced phosphotyrosine enrichment. A combination of well-understood techniques and materials is much more effective than any technique in isolation; but the field of phosphoproteomics currently requires benchmarking of novel materials against current methodologies to fully evaluate their utility in peptide based proteoform analysis.
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Affiliation(s)
- Wen Qiu
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, 310058, Hangzhou, China
| | - Caroline A Evans
- ChELSI Institute, Department of Chemical and Biological Engineering, The University of Sheffield, Mappin Street, Sheffield, S1 3JD, United Kingdom
| | - Andrew Landels
- ChELSI Institute, Department of Chemical and Biological Engineering, The University of Sheffield, Mappin Street, Sheffield, S1 3JD, United Kingdom
| | - Trong Khoa Pham
- ChELSI Institute, Department of Chemical and Biological Engineering, The University of Sheffield, Mappin Street, Sheffield, S1 3JD, United Kingdom
| | - Phillip C Wright
- School of Engineering, Faculty of Science, Agriculture and Engineering, Newcastle University, Newcastle Upon Tyne, NE1 7RU, United Kingdom.
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Genetic determinants of genus-level glycan diversity in a bacterial protein glycosylation system. PLoS Genet 2019; 15:e1008532. [PMID: 31869330 PMCID: PMC6959607 DOI: 10.1371/journal.pgen.1008532] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 01/14/2020] [Accepted: 11/22/2019] [Indexed: 12/27/2022] Open
Abstract
The human pathogens N. gonorrhoeae and N. meningitidis display robust intra- and interstrain glycan diversity associated with their O-linked protein glycosylation (pgl) systems. In an effort to better understand the evolution and function of protein glycosylation operating there, we aimed to determine if other human-restricted, Neisseria species similarly glycosylate proteins and if so, to assess the levels of glycoform diversity. Comparative genomics revealed the conservation of a subset of genes minimally required for O-linked protein glycosylation glycan and established those pgl genes as core genome constituents of the genus. In conjunction with mass spectrometric–based glycan phenotyping, we found that extant glycoform repertoires in N. gonorrhoeae, N. meningitidis and the closely related species N. polysaccharea and N. lactamica reflect the functional replacement of a progenitor glycan biosynthetic pathway. This replacement involved loss of pgl gene components of the primordial pathway coincident with the acquisition of two exogenous glycosyltransferase genes. Critical to this discovery was the identification of a ubiquitous but previously unrecognized glycosyltransferase gene (pglP) that has uniquely undergone parallel but independent pseudogenization in N. gonorrhoeae and N. meningitidis. We suggest that the pseudogenization events are driven by processes of compositional epistasis leading to gene decay. Additionally, we documented instances where inter-species recombination influences pgl gene status and creates discordant genetic interactions due ostensibly to the multi-locus nature of pgl gene networks. In summary, these findings provide a novel perspective on the evolution of protein glycosylation systems and identify phylogenetically informative, genetic differences associated with Neisseria species. Bacteria express a remarkable diversity of sugars and oligosaccharides in conjunction with protein glycosylation systems. Currently however, little is known about the evolutionary processes and selective forces shaping glycan biosynthetic pathways. The closely related bacterial pathogens Neisseria gonorrhoeae and Neisseria meningitidis remain serious sources of human disease and these species express antigenically variable oligosaccharides as components of their broad-spectrum, O‐linked protein glycosylation (pgl) systems. With the exception of isolates of Neisseria elongata subspecies glycolytica, the status of such post-translational modifications in related commensal species colonizing humans remains largely undefined. Here, we exploit new data from further studies of protein glycosylation in Neisseria elongata subspecies glycolytica to address these concerns. Employing comparative genomics and glycan phenotyping, we show that related pgl systems are indeed expressed by all human-restricted Neisseria species but identify unique gene gain and loss events as well as loss-of-function polymorphisms that accommodate a dramatic shift in glycoform structure occurring across the genus. These findings constitute novel perspectives on both the evolution of protein glycosylation systems in general and the macroevolutionary processes occurring in related bacterial species residing within a single host.
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13
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14
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Jalaei J, Layeghi-Ghalehsoukhteh S, Hosseini A, Fazeli M. Antibacterial effects of gold nanoparticles functionalized with the extracted peptide from Vespa orientalis wasp venom. J Pept Sci 2018; 24:e3124. [PMID: 30358026 DOI: 10.1002/psc.3124] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 08/22/2018] [Accepted: 08/31/2018] [Indexed: 01/13/2023]
Abstract
The development of novel antimicrobial strategies is necessary because of the escalation of multidrug-resistant pathogens. Recently, antimicrobial peptides and their combination with nanoparticles were regarded as a promising tool to target drug-resistant pathogens. Herein, we evaluated antimicrobial efficacy of a peptide extracted from Vespa orientalis wasp venom and also its conjugation with gold nanoparticles. Nanoparticle conjugation measurement was done by evaluating the absorbance changes of the surface plasmon resonance band of gold nanoparticles at 555 nm. A significant increase in the antibacterial activity against gram negative and positive bacteria was obtained when the extracted peptide conjugated with gold nanoparticles. Finally, the results show that this new peptide-AuNps has the high practical potential for antibacterial activity and may provide an alternative therapy for bacterial infection.
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Affiliation(s)
- Jafar Jalaei
- Department of Basic Science, School of Veterinary Medicine, Shiraz University, Shiraz, Iran
| | | | - Arsalan Hosseini
- Department of Pathobiology, School of Veterinary Medicine, Shiraz University, Shiraz, Iran
| | - Mehdi Fazeli
- Department of Basic Science, School of Veterinary Medicine, Shiraz University, Shiraz, Iran
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15
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Minic Z, Dahms TES, Babu M. Chromatographic separation strategies for precision mass spectrometry to study protein-protein interactions and protein phosphorylation. J Chromatogr B Analyt Technol Biomed Life Sci 2018; 1102-1103:96-108. [PMID: 30380468 DOI: 10.1016/j.jchromb.2018.10.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 10/19/2018] [Accepted: 10/22/2018] [Indexed: 11/30/2022]
Abstract
Investigating protein-protein interactions and protein phosphorylation can be of great significance when studying biological processes and human diseases at the molecular level. However, sample complexity, presence of low abundance proteins, and dynamic nature of the proteins often impede in achieving sufficient analytical depth in proteomics research. In this regard, chromatographic separation methodologies have played a vital role in the identification and quantification of proteins in complex sample mixtures. The combination of peptide and protein fractionation techniques with advanced high-performance mass spectrometry has allowed the researchers to successfully study the protein-protein interactions and protein phosphorylation. Several new fractionation strategies for large scale analysis of proteins and peptides have been developed to study protein-protein interactions and protein phosphorylation. These emerging chromatography methodologies have enabled the identification of several hundred protein complexes and even thousands of phosphorylation sites in a single study. In this review, we focus on current workflow strategies and chromatographic tools, highlighting their advantages and disadvantages, and examining their associated challenges and future potential.
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Affiliation(s)
- Zoran Minic
- Department of Chemistry and Biomolecular Science, University of Ottawa, John L. Holmes, Mass Spectrometry Facility, 10 Marie-Curie, Marion Hall, Room 02, Ottawa, ON K1N 1A2, Canada.
| | - Tanya E S Dahms
- Department of Chemistry and Biochemistry, University of Regina, 3737 Wascana Parkway, Regina, SK S4S 0A2, Canada
| | - Mohan Babu
- Department of Chemistry and Biochemistry, University of Regina, 3737 Wascana Parkway, Regina, SK S4S 0A2, Canada
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Kanshin E, Pascariu M, Tyers M, D’Amours D, Thibault P. Combined Enrichment/Enzymatic Approach To Study Tightly Clustered Multisite Phosphorylation on Ser-Rich Domains. J Proteome Res 2018; 17:3050-3060. [DOI: 10.1021/acs.jproteome.8b00205] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | | | - Damien D’Amours
- Ottawa Institute of Systems Biology, Department of Cellular and Molecular Medicine, University of Ottawa, Roger Guindon Hall, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
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17
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Couto N, Davlyatova L, Evans CA, Wright PC. Application of the broadband collision-induced dissociation (bbCID) mass spectrometry approach for protein glycosylation and phosphorylation analysis. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2018; 32:75-85. [PMID: 29055059 DOI: 10.1002/rcm.8016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 08/29/2017] [Accepted: 10/10/2017] [Indexed: 06/07/2023]
Abstract
RATIONALE Analysis of post-translationally modified peptides by mass spectrometry (MS) remains incomplete, in part due to incomplete sampling of all peptides which is inherent to traditional data-dependent acquisition (DDA). An alternative MS approach, data-independent acquisition (DIA), enables comprehensive recording of all detectable precursor and product ions, independent of precursor intensity. The use of broadband collision-induced dissociation (bbCID), a DIA method, was evaluated for the identification of protein glycosylation and phosphorylation. METHODS bbCID was applied to identify glycopeptides and phosphopeptides generated from standard proteins using a high-resolution Bruker maXis 3G mass spectrometer. In bbCID, precursor and product ion spectra were obtained by alternating low and high collision energy. Precursor ions were assigned manually based on the detection of diagnostic ions specific to either glycosylation or phosphorylation. The composition of the glycan modification was resolved in the positive ion mode, while the level of phosphorylation was investigated in the negative ion mode. RESULTS The results demonstrate for the first time that the use of a bbCID approach is suitable for the identification of glycopeptides and phosphopeptides based on the detection of specific diagnostic and associated precursor ions. The novel use of bbCID in negative ion mode allowed the discrimination of singly and multiply phosphorylated peptides based on the detection of phosphate diagnostic ions. The results also demonstrate the ability of this approach to allow the identification of glycan composition in N- and O-linked glycopeptides, in positive ion mode. CONCLUSIONS We contend that bbCID is a valuable addition to the existing toolkit for PTM discovery. Moreover, this technique could be employed to direct targeted proteomics methods, particularly where there is no a priori information on glycosylation or phosphorylation status. This technique is immediately relevant to the characterisation of individual proteins or biological samples of low complexity, as demonstrated for the analysis of the glycosylation status of a therapeutic protein.
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Affiliation(s)
- Narciso Couto
- The ChELSI Institute, Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield, S1 3JD, UK
| | - Liliya Davlyatova
- The ChELSI Institute, Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield, S1 3JD, UK
| | - Caroline A Evans
- The ChELSI Institute, Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield, S1 3JD, UK
| | - Phillip C Wright
- The ChELSI Institute, Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield, S1 3JD, UK
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Murillo JR, Goto-Silva L, Sánchez A, Nogueira FCS, Domont GB, Junqueira M. Quantitative proteomic analysis identifies proteins and pathways related to neuronal development in differentiated SH-SY5Y neuroblastoma cells. EUPA OPEN PROTEOMICS 2017; 16:1-11. [PMID: 29900121 PMCID: PMC5965715 DOI: 10.1016/j.euprot.2017.06.001] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 03/07/2017] [Accepted: 06/21/2017] [Indexed: 02/04/2023]
Abstract
Differentiation analysis of SH-SY5Y cells with iTRAQ strategy is proposed. Differentiated SH-SY5Y cells are more appropriated as a neuronal model. Upregulated proteins are mainly related to ECM-interaction and apoptosis. Proteins to explore as differentiation markers: AGRN, EMILIM-1, AIFM, STMN1.
SH-SY5Y neuroblastoma cells are susceptible to differentiation using retinoic acid (RA) and brain-derived neurotrophic factor (BDNF), providing a model of neuronal differentiation. We compared SH-SY5Y cells proteome before and after RA/BDNF treatment using iTRAQ and phosphopeptide enrichment strategies. We identified 5587 proteins, 366 of them with differential abundance. Differentiated cells expressed proteins related to neuronal development, and, undifferentiated cells expressed proteins involved in cell proliferation. Interactive network covered focal adhesion, cytoskeleton dynamics and neurodegenerative diseases processes and regulation of mitogen-activated protein kinase-related signaling pathways; key proteins involved in those processes might be explored as markers for neuronal differentiation.
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Affiliation(s)
- Jimmy Rodriguez Murillo
- Proteomics Unit, Chemistry Institute, Federal University of Rio de Janeiro, 21941-909, Rio de Janeiro, Brazil
| | - Livia Goto-Silva
- D'Or Institute for Research and Education (IDOR), 22281-100, Rio de Janeiro, Brazil
| | - Aniel Sánchez
- Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Skåne University Hospital Malmö, 205 02 Malmö, Sweden.,Center of Excellence in Biological and Medical Mass Spectrometry, Biomedical Center D13, Lund University, 221 84 Lund, Sweden
| | - Fábio C S Nogueira
- Proteomics Unit, Chemistry Institute, Federal University of Rio de Janeiro, 21941-909, Rio de Janeiro, Brazil
| | - Gilberto B Domont
- Proteomics Unit, Chemistry Institute, Federal University of Rio de Janeiro, 21941-909, Rio de Janeiro, Brazil
| | - Magno Junqueira
- Proteomics Unit, Chemistry Institute, Federal University of Rio de Janeiro, 21941-909, Rio de Janeiro, Brazil
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Giorgianni F, Beranova-Giorgianni S. Phosphoproteome Discovery in Human Biological Fluids. Proteomes 2016; 4:proteomes4040037. [PMID: 28248247 PMCID: PMC5260970 DOI: 10.3390/proteomes4040037] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 11/11/2016] [Accepted: 11/23/2016] [Indexed: 01/07/2023] Open
Abstract
Phosphorylation plays a critical role in regulating protein function and thus influences a vast spectrum of cellular processes. With the advent of modern bioanalytical technologies, examination of protein phosphorylation on a global scale has become one of the major research areas. Phosphoproteins are found in biological fluids and interrogation of the phosphoproteome in biological fluids presents an exciting opportunity for discoveries that hold great potential for novel mechanistic insights into protein function in health and disease, and for translation to improved diagnostic and therapeutic approaches for the clinical setting. This review focuses on phosphoproteome discovery in selected human biological fluids: serum/plasma, urine, cerebrospinal fluid, saliva, and bronchoalveolar lavage fluid. Bioanalytical workflows pertinent to phosphoproteomics of biological fluids are discussed with emphasis on mass spectrometry-based approaches, and summaries of studies on phosphoproteome discovery in major fluids are presented.
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Affiliation(s)
- Francesco Giorgianni
- Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, Memphis, TN 38163, USA.
| | - Sarka Beranova-Giorgianni
- Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, Memphis, TN 38163, USA.
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Hernandez-Valladares M, Aasebø E, Selheim F, Berven FS, Bruserud Ø. Selecting Sample Preparation Workflows for Mass Spectrometry-Based Proteomic and Phosphoproteomic Analysis of Patient Samples with Acute Myeloid Leukemia. Proteomes 2016; 4:proteomes4030024. [PMID: 28248234 PMCID: PMC5217354 DOI: 10.3390/proteomes4030024] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 08/09/2016] [Accepted: 08/12/2016] [Indexed: 12/31/2022] Open
Abstract
Global mass spectrometry (MS)-based proteomic and phosphoproteomic studies of acute myeloid leukemia (AML) biomarkers represent a powerful strategy to identify and confirm proteins and their phosphorylated modifications that could be applied in diagnosis and prognosis, as a support for individual treatment regimens and selection of patients for bone marrow transplant. MS-based studies require optimal and reproducible workflows that allow a satisfactory coverage of the proteome and its modifications. Preparation of samples for global MS analysis is a crucial step and it usually requires method testing, tuning and optimization. Different proteomic workflows that have been used to prepare AML patient samples for global MS analysis usually include a standard protein in-solution digestion procedure with a urea-based lysis buffer. The enrichment of phosphopeptides from AML patient samples has previously been carried out either with immobilized metal affinity chromatography (IMAC) or metal oxide affinity chromatography (MOAC). We have recently tested several methods of sample preparation for MS analysis of the AML proteome and phosphoproteome and introduced filter-aided sample preparation (FASP) as a superior methodology for the sensitive and reproducible generation of peptides from patient samples. FASP-prepared peptides can be further fractionated or IMAC-enriched for proteome or phosphoproteome analyses. Herein, we will review both in-solution and FASP-based sample preparation workflows and encourage the use of the latter for the highest protein and phosphorylation coverage and reproducibility.
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Affiliation(s)
- Maria Hernandez-Valladares
- Department of Biomedicine, Faculty of Medicine and Dentistry, University of Bergen, Jonas Lies vei 91, N-5009 Bergen, Norway.
| | - Elise Aasebø
- Department of Biomedicine, Faculty of Medicine and Dentistry, University of Bergen, Jonas Lies vei 91, N-5009 Bergen, Norway.
| | - Frode Selheim
- Department of Biomedicine, Faculty of Medicine and Dentistry, University of Bergen, Jonas Lies vei 91, N-5009 Bergen, Norway.
| | - Frode S Berven
- Department of Biomedicine, Faculty of Medicine and Dentistry, University of Bergen, Jonas Lies vei 91, N-5009 Bergen, Norway.
| | - Øystein Bruserud
- Department of Clinical Science, Faculty of Medicine and Dentistry, University of Bergen, Jonas Lies vei 91, N-5009 Bergen, Norway.
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Aasebø E, Mjaavatten O, Vaudel M, Farag Y, Selheim F, Berven F, Bruserud Ø, Hernandez-Valladares M. Freezing effects on the acute myeloid leukemia cell proteome and phosphoproteome revealed using optimal quantitative workflows. J Proteomics 2016; 145:214-225. [DOI: 10.1016/j.jprot.2016.03.049] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2016] [Revised: 03/23/2016] [Accepted: 03/29/2016] [Indexed: 12/12/2022]
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