1
|
Abyadeh M, Alikhani M, Mirzaei M, Gupta V, Shekari F, Salekdeh GH. Proteomics provides insights into the theranostic potential of extracellular vesicles. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2023; 138:101-133. [PMID: 38220422 DOI: 10.1016/bs.apcsb.2023.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
Extracellular vesicles (EVs) encompass a diverse range of membranous structures derived from cells, including exosomes and microvesicles. These vesicles are present in biological fluids and play vital roles in various physiological and pathological processes. They facilitate intercellular communication by enabling the exchange of proteins, lipids, and genetic material between cells. Understanding the cellular processes that govern EV biology is essential for unraveling their physiological and pathological functions and their potential clinical applications. Despite significant advancements in EV research in recent years, there is still much to learn about these vesicles. The advent of improved mass spectrometry (MS)-based techniques has allowed for a deeper characterization of EV protein composition, providing valuable insights into their roles in different physiological and pathological conditions. In this chapter, we provide an overview of proteomics studies conducted to identify the protein contents of EVs, which contribute to their therapeutic and pathological features. We also provided evidence on the potential of EV proteome contents as biomarkers for early disease diagnosis, progression, and treatment response, as well as factors that influence their composition. Additionally, we discuss the available databases containing information on EV proteome contents, and finally, we highlight the need for further research to pave the way toward their utilization in clinical settings.
Collapse
Affiliation(s)
- Morteza Abyadeh
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Mehdi Alikhani
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Mehdi Mirzaei
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, North Ryde, Sydney, NSW, Australia
| | - Vivek Gupta
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, North Ryde, Sydney, NSW, Australia
| | - Faezeh Shekari
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | | |
Collapse
|
2
|
Dai C, Guo X, Pan Z, Wan C, Yang D, Li Y, Lian C, An Y, Zhang T, Yang F, Zhu L, Yin F, Wang R, Li Z. Pyridinium-Based Strategy for a Bioorthogonal Conjugation-Assisted Purification Method for Profiling Cell Surface Proteome. Anal Chem 2023; 95:17125-17134. [PMID: 37934015 DOI: 10.1021/acs.analchem.3c04279] [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: 11/08/2023]
Abstract
Cell surface proteins (CSPs) are valuable targets for therapeutic agents, but achieving highly selective CSP enrichment in cellular physiology remains a technical challenge. To address this challenge, we propose a newly developed sulfo-pyridinium ester (SPE) cross-linking probe, followed by two-step imaging and enrichment. The SPE probe showed higher efficiency in labeling proteins than similar NHS esters at the level of cell lysates and demonstrated specificity for Lys in competitive experiments. More importantly, this probe could selectively label the cell membranes in cell imaging with only negligible labeling of the intracellular compartment. Moreover, we successfully performed this strategy on MCF-7 live cells to label 425 unique CSPs from 1162 labeled proteins. Finally, we employed our probe to label the CSPs of insulin-cultured MCF-7, revealing several cell surface targets of key functional biomarkers and insulin-associated pathogenesis. The above results demonstrate that the SPE method provides a promising tool for the selective labeling of cell surface proteins and monitoring transient cell surface events.
Collapse
Affiliation(s)
- Chuan Dai
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen 518118, P. R. China
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen 518055, P. R. China
- Department of Pharmacy, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital (Shenzhen Institute of Translational Medicine), Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen 518060, P. R. China
| | - Xiaochun Guo
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen 518055, P. R. China
| | - Zhuoheng Pan
- School of Pharmacy, Macau University of Science and Technology, Taipa 999078, Macau, P. R. China
| | - Chuan Wan
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen 518118, P. R. China
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen 518055, P. R. China
| | - Dongyan Yang
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen 518118, P. R. China
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen 518055, P. R. China
| | - Yongli Li
- China Medical System Holdings Limited, Shenzhen 518055, P. R. China
| | - Chenshan Lian
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen 518118, P. R. China
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen 518055, P. R. China
| | - Yuhao An
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen 518118, P. R. China
| | - Tuanjie Zhang
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen 518118, P. R. China
| | - Fadeng Yang
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen 518055, P. R. China
| | - Lizhi Zhu
- Department of Pharmacy, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital (Shenzhen Institute of Translational Medicine), Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen 518060, P. R. China
| | - Feng Yin
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen 518118, P. R. China
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen 518055, P. R. China
| | - Rui Wang
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen 518118, P. R. China
| | - Zigang Li
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen 518118, P. R. China
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen 518055, P. R. China
- Frontiers Medical Center, Tianfu Jincheng Laboratory, Chengdu 610212, Sichuan, P. R. China
| |
Collapse
|
3
|
Chen Y, An Y, Dai Z, Liu Y, Liang Z, Zhao Q, Zhang L, Zhang Y. Highly selective enrichment of surface proteins from living cells by photo-crosslinking probe enabled in-depth analysis of surfaceome. Anal Chim Acta 2022; 1203:339694. [DOI: 10.1016/j.aca.2022.339694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 03/04/2022] [Accepted: 03/05/2022] [Indexed: 11/01/2022]
|
4
|
Martire S, Montarolo F, Spadaro M, Perga S, Sforza ML, Marozio L, Frezet F, Bruno S, Chiabotto G, Deregibus MC, Camussi G, Botta G, Benedetto C, Bertolotto A. A First Phenotypic and Functional Characterization of Placental Extracellular Vesicles from Women with Multiple Sclerosis. Int J Mol Sci 2021; 22:ijms22062875. [PMID: 33809077 PMCID: PMC8001892 DOI: 10.3390/ijms22062875] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 03/08/2021] [Accepted: 03/09/2021] [Indexed: 12/20/2022] Open
Abstract
Pregnancy is a unique situation of physiological immunomodulation, as well as a strong Multiple Sclerosis (MS) disease modulator whose mechanisms are still unclear. Both maternal (decidua) and fetal (trophoblast) placental cells secrete extracellular vesicles (EVs), which are known to mediate cellular communication and modulate the maternal immune response. Their contribution to the MS disease course during pregnancy, however, is unexplored. Here, we provide a first phenotypic and functional characterization of EVs isolated from cultures of term placenta samples of women with MS, differentiating between decidua and trophoblast. In particular, we analyzed the expression profile of 37 surface proteins and tested the functional role of placental EVs on mono-cultures of CD14+ monocytes and co-cultures of CD4+ T and regulatory T (Treg) cells. Results indicated that placental EVs are enriched for surface markers typical of stem/progenitor cells, and that conditioning with EVs from samples of women with MS is associated to a moderate decrease in the expression of proinflammatory cytokines by activated monocytes and in the proliferation rate of activated T cells co-cultured with Tregs. Overall, our findings suggest an immunomodulatory potential of placental EVs from women with MS and set the stage for a promising research field aiming at elucidating their role in MS remission.
Collapse
Affiliation(s)
- Serena Martire
- Neuroscience Institute Cavalieri Ottolenghi (NICO), Orbassano, 10043 Turin, Italy; (M.S.); (S.P.); (M.L.S.); (A.B.)
- Neurology-CRESM (Regional Reference Center for Multiple Sclerosis), AOU San Luigi Gonzaga, Orbassano, 10043 Turin, Italy
- Correspondence: (S.M.); (F.M.)
| | - Francesca Montarolo
- Neuroscience Institute Cavalieri Ottolenghi (NICO), Orbassano, 10043 Turin, Italy; (M.S.); (S.P.); (M.L.S.); (A.B.)
- Neurology-CRESM (Regional Reference Center for Multiple Sclerosis), AOU San Luigi Gonzaga, Orbassano, 10043 Turin, Italy
- Department of Molecular Biotechnologies and Health Sciences, University of Turin, 10124 Turin, Italy
- Correspondence: (S.M.); (F.M.)
| | - Michela Spadaro
- Neuroscience Institute Cavalieri Ottolenghi (NICO), Orbassano, 10043 Turin, Italy; (M.S.); (S.P.); (M.L.S.); (A.B.)
- Neurology-CRESM (Regional Reference Center for Multiple Sclerosis), AOU San Luigi Gonzaga, Orbassano, 10043 Turin, Italy
| | - Simona Perga
- Neuroscience Institute Cavalieri Ottolenghi (NICO), Orbassano, 10043 Turin, Italy; (M.S.); (S.P.); (M.L.S.); (A.B.)
- Neurology-CRESM (Regional Reference Center for Multiple Sclerosis), AOU San Luigi Gonzaga, Orbassano, 10043 Turin, Italy
- Department of Neuroscience Rita Levi-Montalcini, University of Turin, 10124 Turin, Italy
| | - Maria Ludovica Sforza
- Neuroscience Institute Cavalieri Ottolenghi (NICO), Orbassano, 10043 Turin, Italy; (M.S.); (S.P.); (M.L.S.); (A.B.)
- Neurology-CRESM (Regional Reference Center for Multiple Sclerosis), AOU San Luigi Gonzaga, Orbassano, 10043 Turin, Italy
| | - Luca Marozio
- Department of Surgical Sciences, Obstetrics and Gynaecology, University of Turin, 10124 Turin, Italy; (L.M.); (F.F.); (C.B.)
| | - Federica Frezet
- Department of Surgical Sciences, Obstetrics and Gynaecology, University of Turin, 10124 Turin, Italy; (L.M.); (F.F.); (C.B.)
| | - Stefania Bruno
- Department of Medical Sciences and Molecular Biotechnology Center, University of Turin, 10124 Turin, Italy; (S.B.); (G.C.); (G.C.)
| | - Giulia Chiabotto
- Department of Medical Sciences and Molecular Biotechnology Center, University of Turin, 10124 Turin, Italy; (S.B.); (G.C.); (G.C.)
| | - Maria Chiara Deregibus
- 2i3T Business Incubator and Technology Transfer, University of Turin, 10124 Turin, Italy;
| | - Giovanni Camussi
- Department of Medical Sciences and Molecular Biotechnology Center, University of Turin, 10124 Turin, Italy; (S.B.); (G.C.); (G.C.)
| | - Giovanni Botta
- Department of Pathology, Città della Salute e della Scienza di Torino, 10124 Turin, Italy;
| | - Chiara Benedetto
- Department of Surgical Sciences, Obstetrics and Gynaecology, University of Turin, 10124 Turin, Italy; (L.M.); (F.F.); (C.B.)
| | - Antonio Bertolotto
- Neuroscience Institute Cavalieri Ottolenghi (NICO), Orbassano, 10043 Turin, Italy; (M.S.); (S.P.); (M.L.S.); (A.B.)
- Neurology-CRESM (Regional Reference Center for Multiple Sclerosis), AOU San Luigi Gonzaga, Orbassano, 10043 Turin, Italy
| |
Collapse
|
5
|
Meyfour A, Pahlavan S, Mirzaei M, Krijgsveld J, Baharvand H, Salekdeh GH. The quest of cell surface markers for stem cell therapy. Cell Mol Life Sci 2021; 78:469-495. [PMID: 32710154 PMCID: PMC11073434 DOI: 10.1007/s00018-020-03602-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 07/10/2020] [Accepted: 07/17/2020] [Indexed: 12/15/2022]
Abstract
Stem cells and their derivatives are novel pharmaceutics that have the potential for use as tissue replacement therapies. However, the heterogeneous characteristics of stem cell cultures have hindered their biomedical applications. In theory and practice, when cell type-specific or stage-specific cell surface proteins are targeted by unique antibodies, they become highly efficient in detecting and isolating specific cell populations. There is a growing demand to identify reliable and actionable cell surface markers that facilitate purification of particular cell types at specific developmental stages for use in research and clinical applications. The identification of these markers as very important members of plasma membrane proteins, ion channels, transporters, and signaling molecules has directly benefited from proteomics and tools for proteomics-derived data analyses. Here, we review the methodologies that have played a role in the discovery of cell surface markers and introduce cutting edge single cell proteomics as an advanced tool. We also discuss currently available specific cell surface markers for stem cells and their lineages, with emphasis on the nervous system, heart, pancreas, and liver. The remaining gaps that pertain to the discovery of these markers and how single cell proteomics and identification of surface markers associated with the progenitor stages of certain terminally differentiated cells may pave the way for their use in regenerative medicine are also discussed.
Collapse
Affiliation(s)
- Anna Meyfour
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Sara Pahlavan
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Mehdi Mirzaei
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
- Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW, Australia
| | - Jeroen Krijgsveld
- German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, Heidelberg, Germany
- Medical Faculty, Heidelberg University, Im Neuenheimer Feld 672, Heidelberg, Germany
| | - Hossein Baharvand
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
- Department of Developmental Biology, University of Science and Culture, Tehran, Iran
| | - Ghasem Hosseini Salekdeh
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia.
- Department of Molecular Systems Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Banihashem St, P.O. Box: 16635-148, 1665659911, Tehran, Iran.
| |
Collapse
|
6
|
Li Y, Qin H, Ye M. An overview on enrichment methods for cell surface proteome profiling. J Sep Sci 2019; 43:292-312. [PMID: 31521063 DOI: 10.1002/jssc.201900700] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 09/09/2019] [Accepted: 09/11/2019] [Indexed: 12/17/2022]
Abstract
Cell surface proteins are essential for many important biological processes, including cell-cell interactions, signal transduction, and molecular transportation. With the characteristics of low abundance, high hydrophobicity, and high heterogeneity, it is difficult to get a comprehensive view of cell surface proteome by direct analysis. Thus, it is important to selectively enrich the cell surface proteins before liquid chromatography with mass spectrometry analysis. In recent years, a variety of enrichment methods have been developed. Based on the separation mechanism, these methods could be mainly classified into three types. The first type is based on their difference in the physicochemical property, such as size, density, charge, and hydrophobicity. The second one is based on the bimolecular affinity interaction with lectin or antibody. And the third type is based on the chemical covalent coupling to free side groups of surface-exposed proteins or carbohydrate chains, such as primary amines, carboxyl groups, glycan side chains. In addition, metabolic labeling and enzymatic reaction-based methods have also been employed to selectively isolate cell surface proteins. In this review, we will provide a comprehensive overview of the enrichment methods for cell surface proteome profiling.
Collapse
Affiliation(s)
- Yanan Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, 116023, P. R. China.,University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Hongqiang Qin
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, 116023, P. R. China
| | - Mingliang Ye
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, 116023, P. R. China
| |
Collapse
|