1
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Turner NP. Playing pin-the-tail-on-the-protein in extracellular vesicle (EV) proteomics. Proteomics 2024:e2400074. [PMID: 38899939 DOI: 10.1002/pmic.202400074] [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: 03/15/2024] [Revised: 06/11/2024] [Accepted: 06/12/2024] [Indexed: 06/21/2024]
Abstract
Extracellular vesicles (EVs) are anucleate particles enclosed by a lipid bilayer that are released from cells via exocytosis or direct budding from the plasma membrane. They contain an array of important molecular cargo such as proteins, nucleic acids, and lipids, and can transfer these cargoes to recipient cells as a means of intercellular communication. One of the overarching paradigms in the field of EV research is that EV cargo should reflect the biological state of the cell of origin. The true relationship or extent of this correlation is confounded by many factors, including the numerous ways one can isolate or enrich EVs, overlap in the biophysical properties of different classes of EVs, and analytical limitations. This presents a challenge to research aimed at detecting low-abundant EV-encapsulated nucleic acids or proteins in biofluids for biomarker research and underpins technical obstacles in the confident assessment of the proteomic landscape of EVs that may be affected by sample-type specific or disease-associated proteoforms. Improving our understanding of EV biogenesis, cargo loading, and developments in top-down proteomics may guide us towards advanced approaches for selective EV and molecular cargo enrichment, which could aid EV diagnostics and therapeutics research.
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Affiliation(s)
- Natalie P Turner
- Faculty of Health, Queensland University of Technology, Kelvin Grove, Australia
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2
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Lim W, Lee S, Koh M, Jo A, Park J. Recent advances in chemical biology tools for protein and RNA profiling of extracellular vesicles. RSC Chem Biol 2024; 5:483-499. [PMID: 38846074 PMCID: PMC11151817 DOI: 10.1039/d3cb00200d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 04/25/2024] [Indexed: 06/09/2024] Open
Abstract
Extracellular vesicles (EVs) are nano-sized vesicles secreted by cells that contain various cellular components such as proteins, nucleic acids, and lipids from the parent cell. EVs are abundant in body fluids and can serve as circulating biomarkers for a variety of diseases or as a regulator of various biological processes. Considering these characteristics of EVs, analysis of the EV cargo has been spotlighted for disease diagnosis or to understand biological processes in biomedical research. Over the past decade, technologies for rapid and sensitive analysis of EVs in biofluids have evolved, but detection and isolation of targeted EVs in complex body fluids is still challenging due to the unique physical and biological properties of EVs. Recent advances in chemical biology provide new opportunities for efficient profiling of the molecular contents of EVs. A myriad of chemical biology tools have been harnessed to enhance the analytical performance of conventional assays for better understanding of EV biology. In this review, we will discuss the improvements that have been achieved using chemical biology tools.
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Affiliation(s)
- Woojeong Lim
- Department of Chemistry, Kangwon National University Chuncheon 24341 Korea
| | - Soyeon Lee
- Department of Chemistry, Kangwon National University Chuncheon 24341 Korea
| | - Minseob Koh
- Department of Chemistry, Pusan National University Busan 46241 Republic of Korea
| | - Ala Jo
- Center for Nanomedicine, Institute for Basic Science Seoul 03722 Republic of Korea
| | - Jongmin Park
- Department of Chemistry, Kangwon National University Chuncheon 24341 Korea
- Institute for Molecular Science and Fusion Technology, Kangwon National University Chuncheon 24341 Republic of Korea
- Multidimensional Genomics Research Center, Kangwon National University Chuncheon 24341 Republic of Korea
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3
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Tan J, Zhu C, Li L, Wang J, Xia XH, Wang C. Engineering Cell Membranes: From Extraction Strategies to Emerging Biosensing Applications. Anal Chem 2024; 96:7880-7894. [PMID: 38272835 DOI: 10.1021/acs.analchem.3c01746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2024]
Affiliation(s)
- Jing Tan
- College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, P.R. China
| | - Chengcheng Zhu
- College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, P.R. China
| | - Lulu Li
- College of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang 212000, P.R. China
| | - Jin Wang
- College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, P.R. China
| | - Xing-Hua Xia
- State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing 210023, P.R. China
| | - Chen Wang
- College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, P.R. China
- State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing 210023, P.R. China
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4
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Stollmann A, Garcia-Guirado J, Hong JS, Rüedi P, Im H, Lee H, Ortega Arroyo J, Quidant R. Molecular fingerprinting of biological nanoparticles with a label-free optofluidic platform. Nat Commun 2024; 15:4109. [PMID: 38750038 PMCID: PMC11096335 DOI: 10.1038/s41467-024-48132-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 04/22/2024] [Indexed: 05/18/2024] Open
Abstract
Label-free detection of multiple analytes in a high-throughput fashion has been one of the long-sought goals in biosensing applications. Yet, for all-optical approaches, interfacing state-of-the-art label-free techniques with microfluidics tools that can process small volumes of sample with high throughput, and with surface chemistry that grants analyte specificity, poses a critical challenge to date. Here, we introduce an optofluidic platform that brings together state-of-the-art digital holography with PDMS microfluidics by using supported lipid bilayers as a surface chemistry building block to integrate both technologies. Specifically, this platform fingerprints heterogeneous biological nanoparticle populations via a multiplexed label-free immunoaffinity assay with single particle sensitivity. First, we characterise the robustness and performance of the platform, and then apply it to profile four distinct ovarian cell-derived extracellular vesicle populations over a panel of surface protein biomarkers, thus developing a unique biomarker fingerprint for each cell line. We foresee that our approach will find many applications where routine and multiplexed characterisation of biological nanoparticles are required.
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Affiliation(s)
- Alexia Stollmann
- Nanophotonic Systems Laboratory, Department of Mechanical and Process Engineering, ETH Zurich, 8092, Zurich, Switzerland
| | - Jose Garcia-Guirado
- Nanophotonic Systems Laboratory, Department of Mechanical and Process Engineering, ETH Zurich, 8092, Zurich, Switzerland
| | - Jae-Sang Hong
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Pascal Rüedi
- Nanophotonic Systems Laboratory, Department of Mechanical and Process Engineering, ETH Zurich, 8092, Zurich, Switzerland
| | - Hyungsoon Im
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - Hakho Lee
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - Jaime Ortega Arroyo
- Nanophotonic Systems Laboratory, Department of Mechanical and Process Engineering, ETH Zurich, 8092, Zurich, Switzerland.
| | - Romain Quidant
- Nanophotonic Systems Laboratory, Department of Mechanical and Process Engineering, ETH Zurich, 8092, Zurich, Switzerland.
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5
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Alexandre L, Shen ML, de Araujo LO, Renault J, DeCorwin-Martin P, Martel R, Ng A, Juncker D. Effect of Sample Preprocessing and Size-Based Extraction Methods on the Physical and Molecular Profiles of Extracellular Vesicles. ACS Sens 2024; 9:1239-1251. [PMID: 38436286 PMCID: PMC10964911 DOI: 10.1021/acssensors.3c02070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 02/16/2024] [Accepted: 02/21/2024] [Indexed: 03/05/2024]
Abstract
Extracellular vesicles (EVs) are nanometric lipid vesicles that shuttle cargo between cells. Their analysis could shed light on health and disease conditions, but EVs must first be preserved, extracted, and often preconcentrated. Here we first compare plasma preservation agents, and second, using both plasma and cell supernatant, four EV extraction methods, including (i) ultracentrifugation (UC), (ii) size-exclusion chromatography (SEC), (iii) centrifugal filtration (LoDF), and (iv) accousto-sorting (AcS). We benchmarked them by characterizing the integrity, size distribution, concentration, purity, and expression profiles for nine proteins of EVs, as well as the overall throughput, time-to-result, and cost. We found that the difference between ethylenediaminetetraacetic acid (EDTA) and citrate anticoagulants varies with the extraction method. In our hands, ultracentrifugation produced a high yield of EVs with low contamination; SEC is low-cost, fast, and easy to implement, but the purity of EVs is lower; LoDF and AcS are both compatible with process automation, small volume requirement, and rapid processing times. When using plasma, LoDF was susceptible to clogging and sample contamination, while AcS featured high purity but a lower yield of extraction. Analysis of protein profiles suggests that the extraction methods extract different subpopulations of EVs. Our study highlights the strengths and weaknesses of sample preprocessing methods, and the variability in concentration, purity, and EV expression profiles of the extracted EVs. Preanalytical parameters such as collection or preprocessing protocols must be considered as part of the entire process in order to address EV diversity and their use as clinically actionable indicators.
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Affiliation(s)
- Lucile Alexandre
- Biomedical
Engineering Department, McGill University, Montreal, Quebec H3A 2B4, Canada
- McGill
University & Genome Quebec Innovation Centre, McGill University, Montreal, Quebec H3A 0G1, Canada
- Laboratoire
Physico Chimie Curie, Institut Curie, PSL
Research University, CNRS, 75005 Paris, France
| | - Molly L. Shen
- Biomedical
Engineering Department, McGill University, Montreal, Quebec H3A 2B4, Canada
- McGill
University & Genome Quebec Innovation Centre, McGill University, Montreal, Quebec H3A 0G1, Canada
| | - Lorenna Oliveira
Fernandes de Araujo
- Biomedical
Engineering Department, McGill University, Montreal, Quebec H3A 2B4, Canada
- McGill
University & Genome Quebec Innovation Centre, McGill University, Montreal, Quebec H3A 0G1, Canada
| | - Johan Renault
- Biomedical
Engineering Department, McGill University, Montreal, Quebec H3A 2B4, Canada
- McGill
University & Genome Quebec Innovation Centre, McGill University, Montreal, Quebec H3A 0G1, Canada
| | - Philippe DeCorwin-Martin
- Biomedical
Engineering Department, McGill University, Montreal, Quebec H3A 2B4, Canada
- McGill
University & Genome Quebec Innovation Centre, McGill University, Montreal, Quebec H3A 0G1, Canada
| | - Rosalie Martel
- Biomedical
Engineering Department, McGill University, Montreal, Quebec H3A 2B4, Canada
- McGill
University & Genome Quebec Innovation Centre, McGill University, Montreal, Quebec H3A 0G1, Canada
| | - Andy Ng
- Biomedical
Engineering Department, McGill University, Montreal, Quebec H3A 2B4, Canada
- McGill
University & Genome Quebec Innovation Centre, McGill University, Montreal, Quebec H3A 0G1, Canada
| | - David Juncker
- Biomedical
Engineering Department, McGill University, Montreal, Quebec H3A 2B4, Canada
- McGill
University & Genome Quebec Innovation Centre, McGill University, Montreal, Quebec H3A 0G1, Canada
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6
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Stollmann A, Garcia-Guirado J, Hong JS, Im H, Lee H, Arroyo JO, Quidant R. Molecular fingerprinting of biological nanoparticles with a label-free optofluidic platform. RESEARCH SQUARE 2023:rs.3.rs-3309306. [PMID: 37886549 PMCID: PMC10602063 DOI: 10.21203/rs.3.rs-3309306/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
Label-free detecting multiple analytes in a high-throughput fashion has been one of the long-sought goals in biosensing applications. Yet, for all-optical approaches, interfacing state-of-the-art label-free techniques with microfluidics tools that can process small volumes of sample with high throughput, and with surface chemistry that grants analyte specificity, poses a critical challenge to date. Here, we introduce an optofluidic platform that brings together state-of-the-art digital holography with PDMS microfluidics by using supported lipid bilayers as a surface chemistry building block to integrate both technologies. Specifically, this platform fingerprints heterogeneous biological nanoparticle populations via a multiplexed label-free immunoaffinity assay with single particle sensitivity. Herein, we first thoroughly characterise the robustness and performance of the platform, and then apply it to profile four distinct ovarian cell-derived extracellular vesicle populations over a panel of surface protein biomarkers, thus developing a unique biomarker fingerprint for each cell line. We foresee that our approach will find many applications where routine and multiplexed characterisation of biological nanoparticles is required.
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Affiliation(s)
- Alexia Stollmann
- Nanophotonic Systems Laboratory, Department of Mechanical and Process Engineering, ETH Zurich, 8092 Zurich, Switzerland
| | - Jose Garcia-Guirado
- Nanophotonic Systems Laboratory, Department of Mechanical and Process Engineering, ETH Zurich, 8092 Zurich, Switzerland
| | - Jae-Sang Hong
- Center for Systems Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
| | - Hyungsoon Im
- Center for Systems Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
- Department of Radiology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
| | - Hakho Lee
- Center for Systems Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
- Department of Radiology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
| | - Jaime Ortega Arroyo
- Nanophotonic Systems Laboratory, Department of Mechanical and Process Engineering, ETH Zurich, 8092 Zurich, Switzerland
| | - Romain Quidant
- Nanophotonic Systems Laboratory, Department of Mechanical and Process Engineering, ETH Zurich, 8092 Zurich, Switzerland
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7
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Stollmann A, Garcia-Guirado J, Hong JS, Im H, Lee H, Arroyo JO, Quidant R. Molecular fingerprinting of biological nanoparticles with a label-free optofluidic platform. ARXIV 2023:arXiv:2308.06117v1. [PMID: 37608933 PMCID: PMC10441434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Figures] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Label-free detecting multiple analytes in a high-throughput fashion has been one of the long-sought goals in biosensing applications. Yet, for all-optical approaches, interfacing state-of-the-art label-free techniques with microfluidics tools that can process small volumes of sample with high throughput, and with surface chemistry that grants analyte specificity, poses a critical challenge to date. Here, we introduce an optofluidic platform that brings together state-of-the-art digital holography with PDMS microfluidics by using supported lipid bilayers as a surface chemistry building block to integrate both technologies. Specifically, this platform fingerprints heterogeneous biological nanoparticle populations via a multiplexed label-free immunoaffinity assay with single particle sensitivity. Herein, we first thoroughly characterise the robustness and performance of the platform, and then apply it to profile four distinct ovarian cell-derived extracellular vesicle populations over a panel of surface protein biomarkers, thus developing a unique biomarker fingerprint for each cell line. We foresee that our approach will find many applications where routine and multiplexed characterisation of biological nanoparticles is required.
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Affiliation(s)
- Alexia Stollmann
- Nanophotonic Systems Laboratory, Department of Mechanical and Process Engineering, ETH Zurich, 8092 Zurich, Switzerland
| | - Jose Garcia-Guirado
- Nanophotonic Systems Laboratory, Department of Mechanical and Process Engineering, ETH Zurich, 8092 Zurich, Switzerland
| | - Jae-Sang Hong
- Center for Systems Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
| | - Hyungsoon Im
- Center for Systems Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
- Department of Radiology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
| | - Hakho Lee
- Center for Systems Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
- Department of Radiology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
| | - Jaime Ortega Arroyo
- Nanophotonic Systems Laboratory, Department of Mechanical and Process Engineering, ETH Zurich, 8092 Zurich, Switzerland
| | - Romain Quidant
- Nanophotonic Systems Laboratory, Department of Mechanical and Process Engineering, ETH Zurich, 8092 Zurich, Switzerland
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