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Romanò S, Nele V, Campani V, De Rosa G, Cinti S. A comprehensive guide to extract information from extracellular vesicles: a tutorial review towards novel analytical developments. Anal Chim Acta 2024; 1302:342473. [PMID: 38580402 DOI: 10.1016/j.aca.2024.342473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 03/11/2024] [Accepted: 03/12/2024] [Indexed: 04/07/2024]
Abstract
In the medical field, extracellular vesicles (EVs) are gaining importance as they act as cells mediators. These are phospholipid bilayer vesicles and contain crucial biochemical information about their mother cells being carrier of different biomolecules such as small molecules, proteins, lipids, and nucleic acids. After release into the extracellular matrix, they enter the systemic circulation and can be found in all human biofluids. Since EVs reflect the state of the cell of origin, there is exponential attention as potential source of new circulating biomarkers for liquid biopsy. The use of EVs in clinical practice faces several challenges that need to be addressed: these include the standardization of lysis protocols, the availability of low-cost reagents and the development of analytical tools capable of detecting biomarkers. The process of lysis is a crucial step that can impact all subsequent analyses, towards the development of novel analytical strategies. To aid researchers to support the evolution of measurement science technology, this tutorial review evaluates and discuss the most commonly protocols used to characterize the contents of EVs, including their advantages and disadvantages in terms of experimental procedures, time and equipment. The purpose of this tutorial review is to offer practical guide to researchers which are intended to develop novel analytical approaches. Some of the most significant applications are considered, highlighting their main characteristics divided per mechanism of action. Finally, comprehensive tables which provide an overview at a glance are provided to readers.
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Affiliation(s)
- Sabrina Romanò
- Department of Pharmacy, University of Naples Federico II, Italy.
| | - Valeria Nele
- Department of Pharmacy, University of Naples Federico II, Italy
| | | | | | - Stefano Cinti
- Department of Pharmacy, University of Naples Federico II, Italy.
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Martínez-García J, Villa-Vázquez A, Fernández B, González-Iglesias H, Pereiro R. Exploring capabilities of elemental mass spectrometry for determination of metal and biomolecules in extracellular vesicles. Anal Bioanal Chem 2024; 416:2595-2604. [PMID: 37999724 PMCID: PMC11009778 DOI: 10.1007/s00216-023-05056-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 11/07/2023] [Accepted: 11/13/2023] [Indexed: 11/25/2023]
Abstract
Extracellular vesicles (EVs) are increasingly recognized as crucial components influencing various pathophysiological processes, such as cellular homeostasis, cancer progression, and neurological disease. However, the lack of standardized methods for EV isolation and classification, coupled with ambiguity in biochemical markers associated with EV subtypes, remains a major challenge. This Trends article highlights the most common approaches for EV isolation and characterization, along with recent applications of elemental mass spectrometry (MS) to analyse metals and biomolecules in EVs obtained from biofluids or in vitro cellular models. Considering the promising capabilities of elemental MS, the article also looks ahead to the potential analysis of EVs at the single-vesicle and single-cell levels using ICP-MS. These approaches may offer valuable insights into individual characteristics of EVs and their functions, contributing to a deeper understanding of their role in various biological processes.
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Affiliation(s)
- Jaime Martínez-García
- Department of Physical and Analytical Chemistry, University of Oviedo, Julian Clavería 8, 33006, Oviedo, Spain
| | - Alicia Villa-Vázquez
- Department of Physical and Analytical Chemistry, University of Oviedo, Julian Clavería 8, 33006, Oviedo, Spain
| | - Beatriz Fernández
- Department of Physical and Analytical Chemistry, University of Oviedo, Julian Clavería 8, 33006, Oviedo, Spain.
| | - Héctor González-Iglesias
- Dairy Research Institute of Asturias, Spanish National Research Council (IPLA-CSIC), Villaviciosa, Spain
| | - Rosario Pereiro
- Department of Physical and Analytical Chemistry, University of Oviedo, Julian Clavería 8, 33006, Oviedo, Spain
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Buccini L, Proietti A, La Penna G, Mancini C, Mura F, Tacconi S, Dini L, Rossi M, Passeri D. Toward the nanoscale chemical and physical probing of milk-derived extracellular vesicles using Raman and tip-enhanced Raman spectroscopy. Nanoscale 2024; 16:8132-8142. [PMID: 38568015 DOI: 10.1039/d4nr00845f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Tip-enhanced Raman spectroscopy (TERS) is an advanced technique to perform local chemical analysis of the surface of a sample through the improvement of the sensitivity and the spatial resolution of Raman spectroscopy by plasmonic enhancement of the electromagnetic signal in correspondence with the nanometer-sized tip of an atomic force microscope (AFM). In this work, TERS is demonstrated to represent an innovative and powerful approach for studying extracellular vesicles, in particular bovine milk-derived extracellular vesicles (mEVs), which are nanostructures with considerable potential in drug delivery and therapeutic applications. Raman spectroscopy has been used to analyze mEVs at the micrometric and sub-micrometric scales to obtain a detailed Raman spectrum in order to identify the 'signature' of mEVs in terms of their characteristic molecular vibrations and, therefore, their chemical compositions. With the ability to improve lateral resolution, TERS has been used to study individual mEVs, demonstrating the possibility of investigating a single mEV selected on the surface of the sample and, moreover, analyzing specific locations on the selected mEV with nanometer lateral resolution. TERS potentially allows one to reveal local differences in the composition of mEVs providing new insights into their structure. Also, thanks to the intrinsic properties of TERS to acquire the signal from only the first few nanometers of the surface, chemical investigation of the lipid membrane in correspondence with the various locations of the selected mEV could be performed by analyzing the peaks of the Raman shift in the relevant range of the spectrum (2800-3000 cm-1). Despite being limited to mEVs, this work demonstrates the potential of TERS in the analysis of extracellular vesicles.
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Affiliation(s)
- Luca Buccini
- Department of Basic and Applied Sciences for Engineering, Sapienza University of Rome, Via A. Scarpa 14, 00161 Rome, Italy.
| | - Anacleto Proietti
- Department of Basic and Applied Sciences for Engineering, Sapienza University of Rome, Via A. Scarpa 14, 00161 Rome, Italy.
| | - Giancarlo La Penna
- Department of Basic and Applied Sciences for Engineering, Sapienza University of Rome, Via A. Scarpa 14, 00161 Rome, Italy.
| | - Chiara Mancini
- Department of Basic and Applied Sciences for Engineering, Sapienza University of Rome, Via A. Scarpa 14, 00161 Rome, Italy.
| | - Francesco Mura
- Department of Basic and Applied Sciences for Engineering, Sapienza University of Rome, Via A. Scarpa 14, 00161 Rome, Italy.
- Research Center for Nanotechnology Applied to Engineering of Sapienza University of Rome (CNIS), Piazzale A. Moro 5, 00185 Rome, Italy
| | - Stefano Tacconi
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, 00185 Rome, Italy
| | - Luciana Dini
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, 00185 Rome, Italy
| | - Marco Rossi
- Department of Basic and Applied Sciences for Engineering, Sapienza University of Rome, Via A. Scarpa 14, 00161 Rome, Italy.
- Research Center for Nanotechnology Applied to Engineering of Sapienza University of Rome (CNIS), Piazzale A. Moro 5, 00185 Rome, Italy
| | - Daniele Passeri
- Department of Basic and Applied Sciences for Engineering, Sapienza University of Rome, Via A. Scarpa 14, 00161 Rome, Italy.
- Research Center for Nanotechnology Applied to Engineering of Sapienza University of Rome (CNIS), Piazzale A. Moro 5, 00185 Rome, Italy
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Yao C, Zhang H, Wang C. Recent advances in therapeutic engineered extracellular vesicles. Nanoscale 2024; 16:7825-7840. [PMID: 38533676 DOI: 10.1039/d3nr05470e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/28/2024]
Abstract
Extracellular vesicles (EVs) are natural particles secreted by living cells, which hold significant potential for various therapeutic applications. Native EVs have specific components and structures, allowing them to cross biological barriers, and circulate in vivo for a long time. Native EVs have also been bioengineered to enhance their therapeutic efficacy and targeting affinity. Recently, the therapeutic potential of surface-engineered EVs has been explored in the treatment of tumors, autoimmune diseases, infections and other diseases by ongoing research and clinical trials. In this review, we will introduce the modified methods of engineered EVs, summarize the application of engineered EVs in preclinical and clinical trials, and discuss the opportunities and challenges for the clinical translation of surface-engineered EVs.
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Affiliation(s)
- Chenlu Yao
- Laboratory for Biomaterial and ImmunoEngineering, Institute of Functional Nano & Soft Materials (FUNSOM), Soochow University, Suzhou, Jiangsu 215123, China.
| | - Hong Zhang
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Soochow University, Suzhou, China.
| | - Chao Wang
- Laboratory for Biomaterial and ImmunoEngineering, Institute of Functional Nano & Soft Materials (FUNSOM), Soochow University, Suzhou, Jiangsu 215123, China.
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Jiang S, Tian S, Wang P, Liu J, Sun K, Zhou X, Han Y, Shang Y. Native and engineered extracellular vesicles: novel tools for treating liver disease. J Mater Chem B 2024; 12:3840-3856. [PMID: 38532706 DOI: 10.1039/d3tb01921g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2024]
Abstract
Liver diseases are classified as acute liver damage and chronic liver disease, with recurring liver damage causing liver fibrosis and progression to cirrhosis and hepatoma. Liver transplantation is the only effective treatment for end-stage liver diseases; therefore, novel therapies are required. Extracellular vesicles (EVs) are endogenous nanocarriers involved in cell-to-cell communication that play important roles in immune regulation, tissue repair and regeneration. Native EVs can potentially be used for various liver diseases owing to their high biocompatibility, low immunogenicity and tissue permeability and engineered EVs with surface modification or cargo loading could further optimize therapeutic effects. In this review, we firstly introduced the mechanisms and effects of native EVs derived from different cells and tissues to treat liver diseases of different etiologies. Additionally, we summarized the possible methods to facilitate liver targeting and improve cargo-loading efficiency. In the treatment of liver disease, the detailed engineered methods and the latest delivery strategies were also discussed. Finally, we pointed out the limitations and challenges of EVs for future development and applications. We hope that this review could provide a useful reference for the development of EVs and promote the clinical translation.
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Affiliation(s)
- Shuangshuang Jiang
- State Key Laboratory of Cancer Biology, National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Air Force Military Medical University, Xi'an, 710032, Shaanxi, China.
| | - Siyuan Tian
- State Key Laboratory of Cancer Biology, National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Air Force Military Medical University, Xi'an, 710032, Shaanxi, China.
| | - Punan Wang
- State Key Laboratory of Cancer Biology, National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Air Force Military Medical University, Xi'an, 710032, Shaanxi, China.
| | - Jingyi Liu
- Department of Radiation Oncology, Xijing Hospital, Air Force Military Medical University, Xi'an, 710032, Shaanxi, China
| | - Keshuai Sun
- Department of Gastroenterology, The Air Force Hospital From Eastern Theater of PLA, Nanjing, 210002, Jiangsu, China
| | - Xia Zhou
- State Key Laboratory of Cancer Biology, National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Air Force Military Medical University, Xi'an, 710032, Shaanxi, China.
| | - Ying Han
- State Key Laboratory of Cancer Biology, National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Air Force Military Medical University, Xi'an, 710032, Shaanxi, China.
| | - Yulong Shang
- State Key Laboratory of Cancer Biology, National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Air Force Military Medical University, Xi'an, 710032, Shaanxi, China.
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Chen X, Shen J, Liu C, Shi X, Feng W, Sun H, Zhang W, Zhang S, Jiao Y, Chen J, Hao K, Gao Q, Li Y, Hong W, Wang P, Feng L, Yue S. Applications of Data Characteristic AI-Assisted Raman Spectroscopy in Pathological Classification. Anal Chem 2024; 96:6158-6169. [PMID: 38602477 DOI: 10.1021/acs.analchem.3c04930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2024]
Abstract
Raman spectroscopy has been widely used for label-free biomolecular analysis of cells and tissues for pathological diagnosis in vitro and in vivo. AI technology facilitates disease diagnosis based on Raman spectroscopy, including machine learning (PCA and SVM), manifold learning (UMAP), and deep learning (ResNet and AlexNet). However, it is not clear how to optimize the appropriate AI classification model for different types of Raman spectral data. Here, we selected five representative Raman spectral data sets, including endometrial carcinoma, hepatoma extracellular vesicles, bacteria, melanoma cell, diabetic skin, with different characteristics regarding sample size, spectral data size, Raman shift range, tissue sites, Kullback-Leibler (KL) divergence, and significant Raman shifts (i.e., wavenumbers with significant differences between groups), to explore the performance of different AI models (e.g., PCA-SVM, SVM, UMAP-SVM, ResNet or AlexNet). For data set of large spectral data size, Resnet performed better than PCA-SVM and UMAP. By building data characteristic-assisted AI classification model, we optimized the network parameters (e.g., principal components, activation function, and loss function) of AI model based on data size and KL divergence etc. The accuracy improved from 85.1 to 94.6% for endometrial carcinoma grading, from 77.1 to 90.7% for hepatoma extracellular vesicles detection, from 89.3 to 99.7% for melanoma cell detection, from 88.1 to 97.9% for bacterial identification, from 53.7 to 85.5% for diabetic skin screening, and mean time expense of 5 s.
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Affiliation(s)
- Xun Chen
- Key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education, Institute of Medical Photonics, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
- School of Engineering Medicine, Beihang University, Beijing 100191, China
| | - Jianghao Shen
- Key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education, Institute of Medical Photonics, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| | - Chang Liu
- Key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education, Institute of Medical Photonics, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| | - Xiaoyu Shi
- Department of Obstetrics & Gynecology, Beijing Tiantan Hospital, Capital Medical University, Beijing 100050, China
| | - Weichen Feng
- Key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education, Institute of Medical Photonics, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| | - Hongyi Sun
- Key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education, Institute of Medical Photonics, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| | - Weifeng Zhang
- Key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education, Institute of Medical Photonics, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| | - Shengpai Zhang
- Department of Obstetrics & Gynecology, Beijing Tiantan Hospital, Capital Medical University, Beijing 100050, China
| | - Yuqing Jiao
- Department of Obstetrics & Gynecology, Beijing Tiantan Hospital, Capital Medical University, Beijing 100050, China
| | - Jing Chen
- Su Zhou Surgi-Master High Tech Co., Ltd., Zhangjiagang, Suzhou 215626, China
| | - Kun Hao
- Research and Development Center, Beijing Yaogen Biotechnology Co., Ltd., Beijing 102600, China
| | - Qi Gao
- Research and Development Center, Beijing Yaogen Biotechnology Co., Ltd., Beijing 102600, China
| | - Yitong Li
- Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100021, China
| | - Weili Hong
- Key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education, Institute of Medical Photonics, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| | - Pu Wang
- Key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education, Institute of Medical Photonics, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| | - Limin Feng
- Department of Obstetrics & Gynecology, Beijing Tiantan Hospital, Capital Medical University, Beijing 100050, China
| | - Shuhua Yue
- Key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education, Institute of Medical Photonics, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
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Mishra A, Zehra S, Bharti PK, Mathur SR, Ranjan P, Batra A, Inampudi KK, Modi GP, Nikolajeff F, Kumar S. Spectroscopic insight into breast cancer: profiling small extracellular vesicles lipids via infrared spectroscopy for diagnostic precision. Sci Rep 2024; 14:9347. [PMID: 38654096 DOI: 10.1038/s41598-024-59863-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 04/16/2024] [Indexed: 04/25/2024] Open
Abstract
Breast cancer, a leading cause of female mortality due to delayed detection owing to asymptomatic nature and limited early diagnostic tools, was investigated using a multi-modal approach. Plasma-derived small EVs from breast cancer patients (BrCa, n = 74) and healthy controls (HC, n = 30) were analyzed. Small EVs (n = 104), isolated through chemical precipitation, underwent characterization via transmission electron microscopy (TEM) and nanoparticle tracking analysis (NTA). Validation involved antibody-based tests (TSG101, CD9, CD81, CD63). Infrared spectra of small EVs were obtained, revealing significant differences in lipid acyl chains, particularly in the C-H stretching of CH3. The study focused on the lipid region (3050-2900 cm-1), identifying peaks (3015 cm-1, 2960 cm-1, 2929 cm-1) as distinctive lipid characteristics. Spectroscopic lipid-to-lipid ratios [(I3015/I2929), (I2960/I2929)] emerged as prominent breast cancer markers. Exploration of protein, nucleic acid, and carbohydrate ratios indicated variations in alpha helices, asymmetric C-H stretching vibrations, and C-O stretching at 1033 cm-1. Principal component analysis (PCA) successfully differentiated BrCa and HC small EVs, and heatmap analysis and receiver operating characteristic (ROC) curve evaluations underscored the discriminatory power of lipid ratios. Notably, (I2960/I2929) exhibited 100% sensitivity and specificity, highlighting its potential as a robust BrCa sEV marker for breast cancer detection.
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Affiliation(s)
- Abhay Mishra
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Sadaqa Zehra
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Prahalad Kumar Bharti
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Sandeep R Mathur
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Piyush Ranjan
- Department of Surgical Disciplines, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Atul Batra
- Department of Medical Oncology, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Krishna K Inampudi
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Gyan Prakash Modi
- Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (BHU), Varanasi, 221005, Uttar Pradesh, India
| | - Fredrik Nikolajeff
- Department of Health, Education, and Technology, Lulea University of Technology, 97187, Luleå, Sweden
| | - Saroj Kumar
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, 110029, India.
- Department of Health, Education, and Technology, Lulea University of Technology, 97187, Luleå, Sweden.
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Mohamed NA, Wang Z, Liu Q, Chen P, Su X. Label-Free Light Scattering Imaging with Purified Brownian Motion Differentiates Small Extracellular Vesicles in Cell Microenvironments. Anal Chem 2024; 96:6321-6328. [PMID: 38595097 DOI: 10.1021/acs.analchem.3c05889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
Small extracellular vesicles (sEVs) are heterogeneous biological nanoparticles (NPs) with wide biomedicine applications. Tracking individual nanoscale sEVs can reveal information that conventional microscopic methods may lack, especially in cellular microenvironments. This usually requires biolabeling to identify single sEVs. Here, we developed a light scattering imaging method based on dark-field technology for label-free nanoparticle diffusion analysis (NDA). Compared with nanoparticle tracking analysis (NTA), our method was shown to determine the diffusion probabilities of a single NP. It was demonstrated that accurate size determination of NPs of 41 and 120 nm in diameter is achieved by purified Brownian motion (pBM), without or within the cell microenvironments. Our pBM method was also shown to obtain a consistent size estimation of the normal and cancerous plasma-derived sEVs without and within cell microenvironments, while cancerous plasma-derived sEVs are statistically smaller than normal ones. Moreover, we showed that the velocity and diffusion coefficient are key parameters for determining the diffusion types of the NPs and sEVs in a cancerous cell microenvironment. Our light scattering-based NDA and pBM methods can be used for size determination of NPs, even in cell microenvironments, and also provide a tool that may be used to analyze sEVs for many biomedical applications.
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Affiliation(s)
- Nebras Ahmed Mohamed
- School of Integrated Circuits, Shandong University, Jinan 250101, China
- Institute of Biomedical Engineering, School of Control Science and Engineering, Shandong University, Jinan 250061, China
| | - Zhuo Wang
- School of Integrated Circuits, Shandong University, Jinan 250101, China
- Institute of Biomedical Engineering, School of Control Science and Engineering, Shandong University, Jinan 250061, China
| | - Qiao Liu
- Department of Molecular Medicine and Genetics, School of Basic Medical Sciences, Shandong University, Jinan 250012, China
| | - Pu Chen
- Department of Chemical Engineering, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Xuantao Su
- School of Integrated Circuits, Shandong University, Jinan 250101, China
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Zhang X, Liang M, Song D, Huang R, Chen C, Liu X, Chen H, Wang Q, Sun X, Song J, Zhang J, Kang H, Zeng X. Both protein and non-protein components in extracellular vesicles of human seminal plasma improve human sperm function via CatSper-mediated calcium signaling. Hum Reprod 2024; 39:658-673. [PMID: 38335261 DOI: 10.1093/humrep/deae018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 01/10/2024] [Indexed: 02/12/2024] Open
Abstract
STUDY QUESTION What is the significance and mechanism of human seminal plasma extracellular vesicles (EVs) in regulating human sperm functions? SUMMARY ANSWER EV increases the intracellular Ca2+ concentrations [Ca2+]i via extracellular Ca2+ influx by activating CatSper channels, and subsequently modulate human sperm motility, especially hyperactivated motility, which is attributed to both protein and non-protein components in EV. WHAT IS KNOWN ALREADY EVs are functional regulators of human sperm function, and EV cargoes from normal and asthenozoospermic seminal plasma are different. Pre-fusion of EV with sperm in the acidic and non-physiological sucrose buffer solution could elevate [Ca2+]i in human sperm. CatSper, a principle Ca2+ channel in human sperm, is responsible for the [Ca2+]i regulation when sperm respond to diverse extracellular stimuli. However, the role of CatSper in EV-evoked calcium signaling and its potential physiological significance remain unclear. STUDY DESIGN, SIZE, DURATION EV isolated from the seminal plasma of normal and asthenozoospermic semen were utilized to investigate the mechanism by which EV regulates calcium signal in human sperm, including the involvement of CatSper and the responsible cargoes in EV. In addition, the clinical application potential of EV and EV protein-derived peptides were also evaluated. This is a laboratory study that went on for more than 5 years and involved more than 200 separate experiments. PARTICIPANTS/MATERIALS, SETTING, METHODS Semen donors were recruited in accordance with the Institutional Ethics Committee on human subjects of the Affiliated Hospital of Nantong University and Jiangxi Maternal and Child Health Hospital. The Flow NanoAnalyzer, western blotting, and transmission electron microscope were used to systematically characterize seminal plasma EV. Sperm [Ca2+]i responses were examined by fluorimetric measurement. The whole-cell patch-clamp technique was performed to record CatSper currents. Sperm motility parameters were assessed by computer-assisted sperm analysis. Sperm hyperactivation was also evaluated by examining their penetration ability in viscous methylcellulose media. Protein and non-protein components in EV were analyzed by liquid chromatography-mass spectrum. The levels of prostaglandins, reactive oxygen species, malonaldehyde, and DNA integrity were detected by commercial kits. MAIN RESULTS AND THE ROLE OF CHANCE EV increased [Ca2+]i via an extracellular Ca2+ influx, which could be suppressed by a CatSper inhibitor. Also, EV potentiated CatSper currents in human sperm. Furthermore, the EV-in [Ca2+]i increase and CatSper currents were absent in a CatSper-deficient sperm, confirming the crucial role of CatSper in EV induced Ca2+ signaling in human sperm. Both proteins and non-protein components of EV contributed to the increase of [Ca2+]i, which were important for the effects of EV on human sperm. Consequently, EV and its cargos promoted sperm hyperactivated motility. In addition, seminal plasma EV protein-derived peptides, such as NAT1-derived peptide (N-P) and THBS-1-derived peptide (T-P), could activate the sperm calcium signal and enhance sperm function. Interestingly, EV derived from asthenozoospermic semen caused a lower increase of [Ca2+]i than that isolated from normal seminal plasma (N-EV), and N-EV significantly improved sperm motility and function in both asthenozoospermic samples and frozen-thawed sperm. LARGE SCALE DATA N/A. LIMITATIONS, REASONS FOR CAUTION This was an in vitro study and caution must be taken when extrapolating the physiological relevance to in vivo regulation of sperm. WIDER IMPLICATIONS OF THE FINDINGS Our findings demonstrate that the CatSper-mediated-Ca2+ signaling is involved in EV-modulated sperm function under near physiological conditions, and EV and their derivates are a novel CatSper and sperm function regulators with potential for clinical application. They may be developed to improve sperm motility resulting from low [Ca2+]i response and/or freezing and thawing. STUDY FUNDING/COMPETING INTEREST(S) This research was supported by the National Natural Science Foundation of China (32271167), the Social Development Project of Jiangsu Province (BE2022765), the Nantong Social and People's Livelihood Science and Technology Plan (MS22022087), the Basic Science Research Program of Nantong (JC22022086), and the Jiangsu Innovation and Entrepreneurship Talent Plan (JSSCRC2021543). The authors declare no conflict of interest.
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Affiliation(s)
- Xiaoning Zhang
- Institute of Reproductive Medicine, Medical School, Nantong University, Nantong, China
| | - Min Liang
- Institute of Reproductive Medicine, Medical School, Nantong University, Nantong, China
| | - Dandan Song
- Institute of Life Science and School of Life Science, Nanchang University, Nanchang, China
| | - Rongzu Huang
- Institute of Reproductive Medicine, Medical School, Nantong University, Nantong, China
| | - Chen Chen
- Institute of Reproductive Medicine, Medical School, Nantong University, Nantong, China
| | - Xiaojun Liu
- Institute of Reproductive Medicine, Medical School, Nantong University, Nantong, China
| | - Houyang Chen
- Reproductive Medical Center, Jiangxi Maternal and Child Health Hospital, Nanchang, China
| | - Qingxin Wang
- Department of Obstetrics and Gynecology, Center of Reproductive Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Xiaoli Sun
- Department of Obstetrics and Gynecology, Center of Reproductive Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Jian Song
- Department of Obstetrics and Gynecology, Center of Reproductive Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Jiali Zhang
- Institute of Reproductive Medicine, Medical School, Nantong University, Nantong, China
| | - Hang Kang
- Institute of Reproductive Medicine, Medical School, Nantong University, Nantong, China
| | - Xuhui Zeng
- Institute of Reproductive Medicine, Medical School, Nantong University, Nantong, China
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10
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DiStefano JK, Piras IS, Wu X, Sharma R, Garcia-Mansfield K, Willey M, Lovell B, Pirrotte P, Olson ML, Shaibi GQ. Changes in proteomic cargo of circulating extracellular vesicles in response to lifestyle intervention in adolescents with hepatic steatosis. Clin Nutr ESPEN 2024; 60:333-342. [PMID: 38479932 PMCID: PMC10937812 DOI: 10.1016/j.clnesp.2024.02.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 02/21/2024] [Accepted: 02/22/2024] [Indexed: 03/17/2024]
Abstract
BACKGROUND Recent studies suggest that proteomic cargo of extracellular vesicles (EVs) may play a role in metabolic improvements following lifestyle interventions. However, the relationship between changes in liver fat and circulating EV-derived protein cargo following intervention remains unexplored. METHODS The study cohort comprised 18 Latino adolescents with obesity and hepatic steatosis (12 males/6 females; average age 13.3 ± 1.2 y) who underwent a six-month lifestyle intervention. EV size distribution and concentration were determined by light scattering intensity; EV protein composition was characterized by liquid chromatography tandem-mass spectrometry. RESULTS Average hepatic fat fraction (HFF) decreased 23% by the end of the intervention (12.5% [5.5] to 9.6% [4.9]; P = 0.0077). Mean EV size was smaller post-intervention compared to baseline (120.2 ± 16.4 nm to 128.4 ± 16.5 nm; P = 0.031), although the difference in mean EV concentration (1.1E+09 ± 4.1E+08 particles/mL to 1.1E+09 ± 1.8E+08 particles/mL; P = 0.656)) remained unchanged. A total of 462 proteins were identified by proteomic analysis of plasma-derived EVs from participants pre- and post-intervention, with 113 proteins showing differential abundance (56 higher and 57 lower) between the two timepoints (adj-p <0.05). Pathway analysis revealed enrichment in complement cascade, initial triggering of complement, creation of C4 and C2 activators, and regulation of complement cascade. Hepatocyte-specific EV affinity purification identified 40 proteins with suggestive (p < 0.05) differential abundance between pre- and post-intervention samples. CONCLUSIONS Circulating EV-derived proteins, particularly those associated with the complement cascade, may contribute to improvements in liver fat in response to lifestyle intervention.
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Affiliation(s)
- Johanna K DiStefano
- Diabetes and Metabolic Disease Research Unit, Translational Genomics Research Institute, Phoenix, AZ, USA.
| | - Ignazio S Piras
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Xiumei Wu
- Diabetes and Metabolic Disease Research Unit, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Ritin Sharma
- Integrated Mass Spectrometry Shared Resource, City of Hope Comprehensive Cancer Center, Duarte, CA, USA; Cancer & Cell Biology Division, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Krystine Garcia-Mansfield
- Integrated Mass Spectrometry Shared Resource, City of Hope Comprehensive Cancer Center, Duarte, CA, USA; Cancer & Cell Biology Division, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Maya Willey
- Integrated Mass Spectrometry Shared Resource, City of Hope Comprehensive Cancer Center, Duarte, CA, USA; Cancer & Cell Biology Division, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Brooke Lovell
- Integrated Mass Spectrometry Shared Resource, City of Hope Comprehensive Cancer Center, Duarte, CA, USA; Cancer & Cell Biology Division, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Patrick Pirrotte
- Integrated Mass Spectrometry Shared Resource, City of Hope Comprehensive Cancer Center, Duarte, CA, USA; Cancer & Cell Biology Division, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Micah L Olson
- Division of Endocrinology and Diabetes, Phoenix Children's, Phoenix, AZ, USA; Center for Health Promotion and Disease Prevention, Edson College of Nursing, Arizona State University, Phoenix, AZ, USA
| | - Gabriel Q Shaibi
- Division of Endocrinology and Diabetes, Phoenix Children's, Phoenix, AZ, USA; Center for Health Promotion and Disease Prevention, Edson College of Nursing, Arizona State University, Phoenix, AZ, USA
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11
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Jensen MN, Guerreiro EM, Enciso-Martinez A, Kruglik SG, Otto C, Snir O, Ricaud B, Hellesø OG. Identification of extracellular vesicles from their Raman spectra via self-supervised learning. Sci Rep 2024; 14:6791. [PMID: 38514697 PMCID: PMC10957939 DOI: 10.1038/s41598-024-56788-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 03/11/2024] [Indexed: 03/23/2024] Open
Abstract
Extracellular vesicles (EVs) released from cells attract interest for their possible role in health and diseases. The detection and characterization of EVs is challenging due to the lack of specialized methodologies. Raman spectroscopy, however, has been suggested as a novel approach for biochemical analysis of EVs. To extract information from the spectra, a novel deep learning architecture is explored as a versatile variant of autoencoders. The proposed architecture considers the frequency range separately from the intensity of the spectra. This enables the model to adapt to the frequency range, rather than requiring that all spectra be pre-processed to the same frequency range as it was trained on. It is demonstrated that the proposed architecture accepts Raman spectra of EVs and lipoproteins from 13 biological sources and from two laboratories. High reconstruction accuracy is maintained despite large variances in frequency range and noise level. It is also shown that the architecture is able to cluster the biological nanoparticles by their Raman spectra and differentiate them by their origin without pre-processing of the spectra or supervision during learning. The model performs label-free differentiation, including separating EVs from activated vs. non-activated blood platelets and EVs/lipoproteins from prostate cancer patients versus non-cancer controls. The differentiation is evaluated by creating a neural network classifier that observes the features extracted by the model to classify the spectra according to their sample origin. The classification reveals a test sensitivity of 92.2 % and selectivity of 92.3 % over 769 measurements from two labs that have different measurement configurations.
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Affiliation(s)
- Mathias N Jensen
- Department of Physics and Technology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Eduarda M Guerreiro
- Thrombosis Research Group (TREC), Department of Clinical Medicine, UiT The Arctic University of Norway, Tromsø, Norway
| | - Agustin Enciso-Martinez
- Oncode Institute and Ten Dijke/Chemical Signaling Laboratory, Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
- Amsterdam Vesicle Center, Department of Biomedical Engineering and Physics, Amsterdam University Medical Centers, Amsterdam, The Netherlands
- Laboratory of Experimental Clinical Chemistry, Department of Clinical Chemistry, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Sergei G Kruglik
- CNRS, Institut de Biologie Paris-Seine, Laboratoire Jean Perrin, Sorbonne University, Paris, France
| | - Cees Otto
- Department of Medical Cell BioPhysics, TechMed Centre, University of Twente, Enschede, The Netherlands
| | - Omri Snir
- Thrombosis Research Group (TREC), Department of Clinical Medicine, UiT The Arctic University of Norway, Tromsø, Norway
- Department of Medical Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Benjamin Ricaud
- Department of Physics and Technology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Olav Gaute Hellesø
- Department of Physics and Technology, UiT The Arctic University of Norway, Tromsø, Norway.
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12
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Ito F, Yanatori I, Kato K, Toyokuni S. Protocol for the isolation of GFP-expressing ferroptosis-dependent extracellular vesicles in in vitro cell culture models. STAR Protoc 2024; 5:102892. [PMID: 38363686 PMCID: PMC10877193 DOI: 10.1016/j.xpro.2024.102892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 12/29/2023] [Accepted: 01/30/2024] [Indexed: 02/18/2024] Open
Abstract
Extracellular vesicles (EVs) are complex structures that transport various DNA, RNA, and protein. Recently, new EV secretion mechanisms have been identified through the iron regulatory system in mammalian cells. We revealed that ferroptosis increases EV secretion, which is named ferroptosis-dependent EVs (FedEVs). Here, we describe a step-by-step procedure to isolate GFP-expressing FedEVs for in vitro analysis. The FedEVs are further analyzed by imaging and flow cytometry analysis. For complete details on the use and execution of this protocol, please refer to Ito et al.1.
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Affiliation(s)
- Fumiya Ito
- Department of Pathology and Biological Responses, Nagoya University Graduate School of Medicine, 65 Tsurumai-Cho, Showa-ku, Nagoya 466-8550, Japan; Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
| | - Izumi Yanatori
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Katsuhiro Kato
- Department of Cardiology, Nagoya University Graduate School of Medicine, 65, Tsurumai-Cho, Showa-ku, Nagoya 466-8550, Japan
| | - Shinya Toyokuni
- Department of Pathology and Biological Responses, Nagoya University Graduate School of Medicine, 65 Tsurumai-Cho, Showa-ku, Nagoya 466-8550, Japan.
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13
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Yang S, Zheng B, Raza F, Zhang S, Yuan WE, Su J, Qiu M. Tumor-derived microvesicles for cancer therapy. Biomater Sci 2024; 12:1131-1150. [PMID: 38284828 DOI: 10.1039/d3bm01980b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2024]
Abstract
Extracellular vesicles (EVs) are vesicles with lipid bilayer structures shed from the plasma membrane of cells. Microvesicles (MVs) are a subset of EVs containing proteins, lipids, nucleic acids, and other metabolites. MVs can be produced under specific cell stimulation conditions and isolated by modern separation technology. Due to their tumor homing and large volume, tumor cell-derived microvesicles (TMVs) have attracted interest recently and become excellent delivery carriers for therapeutic vaccines, imaging agents or antitumor drugs. However, preparing sufficient and high-purity TMVs and conducting clinical transformation has become a challenge in this field. In this review, the recent research achievements in the generation, isolation, characterization, modification, and application of TMVs in cancer therapy are reviewed, and the challenges facing therapeutic applications are also highlighted.
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Affiliation(s)
- Shiqi Yang
- School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, 200240, Shanghai, China.
| | - Bo Zheng
- School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, 200240, Shanghai, China.
| | - Faisal Raza
- School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, 200240, Shanghai, China.
| | - Shulei Zhang
- School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, 200240, Shanghai, China.
| | - Wei-En Yuan
- School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, 200240, Shanghai, China.
- Engineering Research Center of Cell & Therapeuti c Antibody, Ministry of Education, and School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jing Su
- School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, 200240, Shanghai, China.
| | - Mingfeng Qiu
- School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Road, 200240, Shanghai, China.
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14
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Bu Y, Wang J, Ni S, Lu Z, Guo Y, Yobas L. High-Performance Gel-Free and Label-Free Size Fractionation of Extracellular Vesicles with Two-Dimensional Electrophoresis in a Microfluidic Artificial Sieve. Anal Chem 2024; 96:3508-3516. [PMID: 38364051 DOI: 10.1021/acs.analchem.3c05290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2024]
Abstract
Extracellular vesicles (EVs) are cell-derived particles that exhibit diverse sizes, molecular contents, and clinical implications for various diseases depending on their specific subpopulations. However, fractionation of EV subpopulations with high resolution, efficiency, purity, and yield remains an elusive goal due to their diminutive sizes. In this study, we introduce a novel strategy that effectively separates EV subpopulations in a gel-free and label-free manner, using two-dimensional (2D) electrophoresis in a microfluidic artificial sieve. The microfabricated artificial sieve consists of periodically arranged micro-slit-well structures in a 2D array and generates an anisotropic electric field pattern to size fractionate EVs into discrete streams and steer the subpopulations into designated outlets for collection within a minute. Along with fractionating EV subpopulations, contaminants such as free proteins and short nucleic acids can be simultaneously directed to waste outlets, thus accomplishing both size fractionation and purification of EVs with high performance. Our platform offers a simple, rapid, and versatile solution for EV subpopulation isolation, which can potentially facilitate the discovery of biomarkers for specific EV subtypes and the development of EV-based therapeutics.
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Affiliation(s)
- Yang Bu
- Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong SAR 999077, P. R. China
| | - Jinhui Wang
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong SAR 999077, P. R. China
| | - Sheng Ni
- Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong SAR 999077, P. R. China
| | - Zechen Lu
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong SAR 999077, P. R. China
| | - Yusong Guo
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong SAR 999077, P. R. China
| | - Levent Yobas
- Department of Electronic and Computer Engineering, Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong SAR 999077, P. R. China
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15
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Ciferri MC, Bruno S, Rosenwasser N, Gorgun C, Reverberi D, Gagliani MC, Cortese K, Grange C, Bussolati B, Quarto R, Tasso R. Standardized Method to Functionalize Plasma-Extracellular Vesicles via Copper-Free Click Chemistry for Targeted Drug Delivery Strategies. ACS Appl Bio Mater 2024; 7:827-838. [PMID: 38227342 DOI: 10.1021/acsabm.3c00822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2024]
Abstract
Extracellular vesicles (EVs) have emerged as potential vehicles for targeted drug delivery and diagnostic applications. However, achieving consistent and reliable functionalization of EV membranes remains a challenge. Copper-catalyzed click chemistry, commonly used for EV surface modification, poses limitations due to cytotoxicity and interference with biological systems. To overcome these limitations, we developed a standardized method for functionalizing an EV membrane via copper-free click chemistry. EVs derived from plasma hold immense potential as diagnostic and therapeutic agents. However, the isolation and functionalization of EVs from such a complex biofluid represent considerable challenges. We compared three different EV isolation methods to obtain an EV suspension with an optimal purity/yield ratio, and we identified sucrose cushion ultracentrifugation (sUC) as the ideal protocol. We then optimized the reaction conditions to successfully functionalize the plasma-EV surface through a copper-free click chemistry strategy with a fluorescently labeled azide, used as a proof-of-principle molecule. Click-EVs maintained their identity, size, and, more importantly, capacity to be efficiently taken up by responder tumor cells. Moreover, once internalized, click EVs partially followed the endosomal recycling route. The optimized reaction conditions and characterization techniques presented in this study offer a foundation for future investigations and applications of functionalized EVs in drug delivery, diagnostics, and therapeutics.
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Affiliation(s)
- Maria Chiara Ciferri
- Department of Experimental Medicine, University of Genova, Largo Rosanna Benzi 10, Genova 16132, Italy
| | - Silvia Bruno
- Department of Experimental Medicine, University of Genova, Largo Rosanna Benzi 10, Genova 16132, Italy
| | - Nicole Rosenwasser
- Department of Experimental Medicine, University of Genova, Largo Rosanna Benzi 10, Genova 16132, Italy
| | - Cansu Gorgun
- Department of Experimental Medicine, University of Genova, Largo Rosanna Benzi 10, Genova 16132, Italy
| | - Daniele Reverberi
- UO Molecular Pathology, IRCCS Ospedale Policlinico San Martino, Largo Rosanna Benzi 10, Genova 16132, Italy
| | - Maria Cristina Gagliani
- Department of Experimental Medicine, University of Genova, Largo Rosanna Benzi 10, Genova 16132, Italy
| | - Katia Cortese
- Department of Experimental Medicine, University of Genova, Largo Rosanna Benzi 10, Genova 16132, Italy
| | - Cristina Grange
- Department of Medical Sciences, University of Torino, Via Nizza 52, Torino 10126, Italy
| | - Benedetta Bussolati
- UO Cellular Oncology, IRCCS Ospedale Policlinico San Martino, Largo Rosanna Benzi 10, Genova 16132, Italy
| | - Rodolfo Quarto
- Department of Experimental Medicine, University of Genova, Largo Rosanna Benzi 10, Genova 16132, Italy
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino 10126, Italy
| | - Roberta Tasso
- Department of Experimental Medicine, University of Genova, Largo Rosanna Benzi 10, Genova 16132, Italy
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino 10126, Italy
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16
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Chen W, Sun J, Mao Y, Tang Y, Wang J, Liu Z. Endogenously Gated DNA Walking Machine for Prescreened MicroRNA Detection in Extracellular Vesicles. Anal Chem 2024; 96:2244-2252. [PMID: 38253329 DOI: 10.1021/acs.analchem.3c05595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Tumor-derived extracellular vesicle (T-EV) microRNAs have been investigated as promising biomarkers in clinical diagnosis as well as disease progression monitoring. However, the expression profiles of microRNA in different tissues vary widely, the precise monitoring of microRNA levels in EVs originating from diseased tissues is susceptible to background interference, thus remains a challenge. Conventional assays require extensive processing, such as EV isolation and even sample lysis, which is both slow and laborious, and the cumbersome pretreatment could spoil the downstream analysis. To address this issue, we developed a generalizable strategy for T-EVs-selective activation and therefore specific amplified microRNA imaging. The conditional signal amplification is established by integrating a traditional DNA walker system with endogenously activated motif to achieve sensitized microRNA imaging in T-EVs. The preorganized endogenous activation with additional sensing criteria narrowed the scope against the complex specimens, and the amplified sensing with reduced off-target signals was supposed to be sensitive to monitor the tiny changes of microRNA expression during the disease course, which holds great potential for accurate diagnosis and prognosis.
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Affiliation(s)
- Weiming Chen
- College of Health Science and Engineering, Key Laboratory for the Synthesis and Application of Organic Functional Molecules (Ministry of Education), Hubei University, Wuhan 430062, P. R. China
| | - Jiale Sun
- College of Health Science and Engineering, Key Laboratory for the Synthesis and Application of Organic Functional Molecules (Ministry of Education), Hubei University, Wuhan 430062, P. R. China
| | - Yuqing Mao
- College of Health Science and Engineering, Key Laboratory for the Synthesis and Application of Organic Functional Molecules (Ministry of Education), Hubei University, Wuhan 430062, P. R. China
| | - Yuhao Tang
- College of Health Science and Engineering, Key Laboratory for the Synthesis and Application of Organic Functional Molecules (Ministry of Education), Hubei University, Wuhan 430062, P. R. China
| | - Jing Wang
- College of Health Science and Engineering, Key Laboratory for the Synthesis and Application of Organic Functional Molecules (Ministry of Education), Hubei University, Wuhan 430062, P. R. China
| | - Zhihong Liu
- College of Health Science and Engineering, Key Laboratory for the Synthesis and Application of Organic Functional Molecules (Ministry of Education), Hubei University, Wuhan 430062, P. R. China
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17
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Thomas S, Kaur J, Kamboj R, Thangariyal S, Yadav R, Kumar K, Dhania NK. Investigate the efficacy of size exclusion chromatography for the isolation of extracellular vesicles from C. elegans. J Chromatogr B Analyt Technol Biomed Life Sci 2024; 1233:123982. [PMID: 38176095 DOI: 10.1016/j.jchromb.2023.123982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 12/06/2023] [Accepted: 12/20/2023] [Indexed: 01/06/2024]
Abstract
Isolation of Extracellular Vesicles (EVs) has been done extensively in the past using ultracentrifugation, a recent shift has been observed towards precipitation, and exosome isolation kits. These methods often co-elute contaminants of similar size and density which makes their detection and downstream applications quite challenging. As well as the EV yield is also compromised in some methodologies due to aggregate formation. In recent reports, size-exclusion chromatography (SEC) is replacing density gradient-based ultracentrifugation as the gold standard of exosome isolation. It outperforms in yield, purity and does not account for any physical damage to the EVs. We have standardized the methodology for an efficient pure yield of homogenous exosomes of size even smaller than 75 nm in Caenorhabditis elegans homogenate. The paper entails the application and optimization of EV isolation by SEC based on previous studies by optimizing bed size and type of sepharose column employed. We propose that this method is economically feasible in comparison with currently available approaches. A comparative study was conducted to investigate the performance of CL-6B in relation to CL-2B and further, this was combined with ultracentrifugation for higher efficacy. The methodology could be introduced in a clinical setting due to its therapeutic potential and scope. The eluted EVs were studied by flow cytometry, nanotracking and characterized for size and morphology.
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Affiliation(s)
- Sharon Thomas
- Department of Zoology, Faculty of Sciences, University of Delhi, Delhi 110007, India
| | - Jaspreet Kaur
- Department of Zoology, Faculty of Sciences, University of Delhi, Delhi 110007, India
| | - Robinsh Kamboj
- USIC, Faculty of Sciences, University of Delhi, Delhi 110007, India
| | - Swati Thangariyal
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, Delhi 110070, India
| | - Rahul Yadav
- Department of Chemistry, Indian Institute of Technology, New Delhi, Delhi 110016, India
| | - Kamlesh Kumar
- Department of Chemistry, Kirori Mal College, University of Delhi, Delhi 110007, India
| | - Narender K Dhania
- Department of Zoology, Faculty of Sciences, University of Delhi, Delhi 110007, India.
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18
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Perpiñá-Clérigues C, Mellado S, Galiana-Roselló C, Fernández-Regueras M, Marcos M, García-García F, Pascual M. Novel insight into the lipid network of plasma extracellular vesicles reveal sex-based differences in the lipidomic profile of alcohol use disorder patients. Biol Sex Differ 2024; 15:10. [PMID: 38273378 PMCID: PMC10809459 DOI: 10.1186/s13293-024-00584-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 01/11/2024] [Indexed: 01/27/2024] Open
Abstract
BACKGROUND Alcohol use disorder (AUD) is one of the most common psychiatric disorders, with the consumption of alcohol considered a leading cause of preventable deaths worldwide. Lipids play a crucial functional role in cell membranes; however, we know little about the role of lipids in extracellular vesicles (EVs) as regulatory molecules and disease biomarkers. METHODS We employed a sensitive lipidomic strategy to characterize lipid species from the plasma EVs of AUD patients to evaluate functional roles and enzymatic activity networks to improve the knowledge of lipid metabolism after alcohol consumption. We analyzed plasma EV lipids from AUD females and males and healthy individuals to highlight lipids with differential abundance and biologically interpreted lipidomics data using LINEX2, which evaluates enzymatic dysregulation using an enrichment algorithm. RESULTS Our results show, for the first time, that AUD females exhibited more significant substrate-product changes in lysophosphatidylcholine/phosphatidylcholine lipids and phospholipase/acyltransferase activity, which are potentially linked to cancer progression and neuroinflammation. Conversely, AUD males suffer from dysregulated ceramide and sphingomyelin lipids involving sphingomyelinase, sphingomyelin phosphodiesterase, and sphingomyelin synthase activity, which relates to hepatotoxicity. Notably, the analysis of plasma EVs from AUD females and males demonstrates enrichment of lipid ontology terms associated with "negative intrinsic curvature" and "positive intrinsic curvature", respectively. CONCLUSIONS Our methodological developments support an improved understanding of lipid metabolism and regulatory mechanisms, which contribute to the identification of novel lipid targets and the discovery of sex-specific clinical biomarkers in AUD.
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Affiliation(s)
- Carla Perpiñá-Clérigues
- Computational Biomedicine Laboratory, Príncipe Felipe Research Center, C/Eduardo Primo Yúfera, 3, 46012, Valencia, Spain
- Department of Physiology, School of Medicine and Dentistry, University of Valencia, Avda. Blasco Ibáñez, 15, 46010, Valencia, Spain
| | - Susana Mellado
- Department of Physiology, School of Medicine and Dentistry, University of Valencia, Avda. Blasco Ibáñez, 15, 46010, Valencia, Spain
| | - Cristina Galiana-Roselló
- Department of Inorganic Chemistry, Institute of Molecular Science, University of Valencia, 46980, Paterna, Spain
| | - María Fernández-Regueras
- Hospital Universitario de Burgos, 09006, Burgos, Spain
- Hospital Universitario de Salamanca, 37007, Salamanca, Spain
| | - Miguel Marcos
- Department of Internal Medicine, University Hospital of Salamanca, University of Salamanca, Institute of Biomedical Research of Salamanca (IBSAL), 37007, Salamanca, Spain
| | - Francisco García-García
- Computational Biomedicine Laboratory, Príncipe Felipe Research Center, C/Eduardo Primo Yúfera, 3, 46012, Valencia, Spain.
| | - María Pascual
- Department of Physiology, School of Medicine and Dentistry, University of Valencia, Avda. Blasco Ibáñez, 15, 46010, Valencia, Spain.
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19
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Lokumcu T, Iskar M, Schneider M, Helm D, Klinke G, Schlicker L, Bethke F, Müller G, Richter K, Poschet G, Phillips E, Goidts V. Proteomic, Metabolomic, and Fatty Acid Profiling of Small Extracellular Vesicles from Glioblastoma Stem-Like Cells and Their Role in Tumor Heterogeneity. ACS Nano 2024; 18:2500-2519. [PMID: 38207106 PMCID: PMC10811755 DOI: 10.1021/acsnano.3c11427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 12/27/2023] [Accepted: 01/02/2024] [Indexed: 01/13/2024]
Abstract
Glioblastoma is a deadly brain tumor for which there is no cure. The presence of glioblastoma stem-like cells (GSCs) contributes to the heterogeneous nature of the disease and makes developing effective therapies challenging. Glioblastoma cells have been shown to influence their environment by releasing biological nanostructures known as extracellular vesicles (EVs). Here, we investigated the role of GSC-derived nanosized EVs (<200 nm) in glioblastoma heterogeneity, plasticity, and aggressiveness, with a particular focus on their protein, metabolite, and fatty acid content. We showed that conditioned medium and small extracellular vesicles (sEVs) derived from cells of one glioblastoma subtype induced transcriptomic and proteomic changes in cells of another subtype. We found that GSC-derived sEVs are enriched in proteins playing a role in the transmembrane transport of amino acids, carboxylic acids, and organic acids, growth factor binding, and metabolites associated with amino acid, carboxylic acid, and sugar metabolism. This suggests a dual role of GSC-derived sEVs in supplying neighboring GSCs with valuable metabolites and proteins responsible for their transport. Moreover, GSC-derived sEVs were enriched in saturated fatty acids, while their respective cells were high in unsaturated fatty acids, supporting that the loading of biological cargos into sEVs is a highly regulated process and that GSC-derived sEVs could be sources of saturated fatty acids for the maintenance of glioblastoma cell metabolism. Interestingly, sEVs isolated from GSCs of the proneural and mesenchymal subtypes are enriched in specific sets of proteins, metabolites, and fatty acids, suggesting a molecular collaboration between transcriptionally different glioblastoma cells. In summary, this study revealed the complexity of GSC-derived sEVs and unveiled their potential contribution to tumor heterogeneity and critical cellular processes commonly deregulated in glioblastoma.
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Affiliation(s)
- Tolga Lokumcu
- Brain
Tumor Translational Targets, German Cancer
Research Center (DKFZ), Heidelberg 69120, Germany
- Faculty
of Biosciences, University of Heidelberg, Heidelberg 69120, Germany
| | - Murat Iskar
- Friedrich
Miescher Institute for Biomedical Research, Basel 4058, Switzerland
| | - Martin Schneider
- Proteomics
Core Facility, German Cancer Research Center
(DKFZ), Heidelberg 69120, Germany
| | - Dominic Helm
- Proteomics
Core Facility, German Cancer Research Center
(DKFZ), Heidelberg 69120, Germany
| | - Glynis Klinke
- Metabolomics
Core Technology Platform, Centre for Organismal Studies, Heidelberg University, Heidelberg 69120, Germany
| | - Lisa Schlicker
- Proteomics
Core Facility, German Cancer Research Center
(DKFZ), Heidelberg 69120, Germany
- Division
of Tumor Metabolism and Microenvironment, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Frederic Bethke
- Brain
Tumor Translational Targets, German Cancer
Research Center (DKFZ), Heidelberg 69120, Germany
| | - Gabriele Müller
- Brain
Tumor Translational Targets, German Cancer
Research Center (DKFZ), Heidelberg 69120, Germany
| | - Karsten Richter
- Core
Facility Electron Microscopy, German Cancer
Research Center (DKFZ), Heidelberg 69120, Germany
| | - Gernot Poschet
- Metabolomics
Core Technology Platform, Centre for Organismal Studies, Heidelberg University, Heidelberg 69120, Germany
| | - Emma Phillips
- Brain
Tumor Translational Targets, German Cancer
Research Center (DKFZ), Heidelberg 69120, Germany
| | - Violaine Goidts
- Brain
Tumor Translational Targets, German Cancer
Research Center (DKFZ), Heidelberg 69120, Germany
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20
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Di Santo R, Niccolini B, Romanò S, Vaccaro M, Di Giacinto F, De Spirito M, Ciasca G. Advancements in Mid-Infrared spectroscopy of extracellular vesicles. Spectrochim Acta A Mol Biomol Spectrosc 2024; 305:123346. [PMID: 37774583 DOI: 10.1016/j.saa.2023.123346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 08/07/2023] [Accepted: 09/02/2023] [Indexed: 10/01/2023]
Abstract
Extracellular vesicles (EVs) are lipid vesicles secreted by all cells into the extracellular space and act as nanosized biological messengers among cells. They carry a specific molecular cargo, composed of lipids, proteins, nucleic acids, and carbohydrates, which reflects the state of their parent cells. Due to their remarkable structural and compositional heterogeneity, characterizing EVs, particularly from a biochemical perspective, presents complex challenges. In this context, mid-infrared (IR) spectroscopy is emerging as a valuable tool, providing researchers with a comprehensive and label-free spectral fingerprint of EVs in terms of their specific molecular content. This review aims to provide an up-to-date critical overview of the major advancements in mid-IR spectroscopy of extracellular vesicles, encompassing both fundamental and applied research achievements. We also systematically emphasize the new possibilities offered by the integration of emerging cutting-edge IR technologies, such as tip-enhanced and surface-enhanced spectroscopy approaches, along with the growing use of machine learning for data analysis and spectral interpretation. Additionally, to assist researchers in navigating this intricate subject, our manuscript includes a wide and detailed collection of the spectral peaks that have been assigned to EV molecular constituents up to now in the literature.
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Affiliation(s)
- Riccardo Di Santo
- Dipartimento di Neuroscienze, Sezione di Fisica, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; Fondazione Policlinico Universitario "A. Gemelli" IRCCS, 00168 Rome, Italy.
| | - Benedetta Niccolini
- Dipartimento di Neuroscienze, Sezione di Fisica, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Sabrina Romanò
- Dipartimento di Neuroscienze, Sezione di Fisica, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Maria Vaccaro
- Fondazione Policlinico Universitario "A. Gemelli" IRCCS, 00168 Rome, Italy
| | - Flavio Di Giacinto
- Dipartimento di Neuroscienze, Sezione di Fisica, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; Fondazione Policlinico Universitario "A. Gemelli" IRCCS, 00168 Rome, Italy
| | - Marco De Spirito
- Dipartimento di Neuroscienze, Sezione di Fisica, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; Fondazione Policlinico Universitario "A. Gemelli" IRCCS, 00168 Rome, Italy
| | - Gabriele Ciasca
- Dipartimento di Neuroscienze, Sezione di Fisica, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; Fondazione Policlinico Universitario "A. Gemelli" IRCCS, 00168 Rome, Italy
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21
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Hsia T, You DG, Politis MG, Batool SM, Ekanayake E, Lee H, Carter BS, Balaj L. Rigorous Comparison of Extracellular Vesicle Processing to Enhance Downstream Analysis for Glioblastoma Characterization. Adv Biol (Weinh) 2024; 8:e2300233. [PMID: 37670402 DOI: 10.1002/adbi.202300233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 07/28/2023] [Indexed: 09/07/2023]
Abstract
Extracellular vesicles (EVs) are highly sought after as a source of biomarkers for disease detection and monitoring. Tumor EV isolation, processing, and evaluation from biofluids is convoluted by EV heterogeneity and biological contaminants and is limited by technical processing efficacy. This study rigorously compares common bulk EV isolation workflows (size exclusion chromatography, SEC; membrane affinity, MA) alongside downstream RNA extraction protocols to investigate molecular analyte recovery. EV integrity and recovery is evaluated using a variety of technologies to quantify total intact EVs, total and surface proteins, and RNA purity and recovery. A comprehensive evaluation of each analyte is performed, with a specific emphasis on maintaining user (n = 2), biological (n = 3), and technical replicates (n≥3) under in vitro conditions. Subsequent study of tumor EV spike-in into healthy donor plasma samples is performed to further validate biofluid-derived EV purity and isolation for clinical application. Results show that EV surface integrity is considerably preserved in eluates from SEC-derived EVs, but RNA recovery and purity, as well as bulk protein isolation, is significantly improved in MA-isolated EVs. This study concludes that EV isolation and RNA extraction pipelines govern recovered analyte integrity, necessitating careful selection of processing modality to enhance recovery of the analyte of interest.
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Affiliation(s)
- Tiffaney Hsia
- Department of Neurosurgery, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA, 02114, USA
| | - Dong Gil You
- Department of Neurosurgery, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA, 02114, USA
| | - Michelle Garlin Politis
- Center for Systems Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA, 02114, USA
| | - Syeda Maheen Batool
- Department of Neurosurgery, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA, 02114, USA
| | - Emil Ekanayake
- Department of Neurosurgery, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA, 02114, USA
| | - Hakho Lee
- Center for Systems Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA, 02114, USA
- Department of Radiology, Massachusetts General Hospital, 55 Fruit Street, Boston, MA, 02114, USA
| | - Bob S Carter
- Department of Neurosurgery, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA, 02114, USA
- Department of Neurosurgery, Harvard Medical School, 25 Shattuck Street, Boston, MA, 02115, USA
| | - Leonora Balaj
- Department of Neurosurgery, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA, 02114, USA
- Department of Neurosurgery, Harvard Medical School, 25 Shattuck Street, Boston, MA, 02115, USA
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22
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Stastna M. Advances in separation and identification of biologically important milk proteins and peptides. Electrophoresis 2024; 45:101-119. [PMID: 37289082 DOI: 10.1002/elps.202300084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 05/30/2023] [Accepted: 05/30/2023] [Indexed: 06/09/2023]
Abstract
Milk is a rich source of biologically important proteins and peptides. In addition, milk contains a variety of extracellular vesicles (EVs), including exosomes, that carry their own proteome cargo. EVs are essential for cell-cell communication and modulation of biological processes. They act as nature carriers of bioactive proteins/peptides in targeted delivery during various physiological and pathological conditions. Identification of the proteins and protein-derived peptides in milk and EVs and recognition of their biological activities and functions had a tremendous impact on food industry, medicine research, and clinical applications. Advanced separation methods, mass spectrometry (MS)-based proteomic approaches and innovative biostatistical procedures allowed for characterization of milk protein isoforms, genetic/splice variants, posttranslational modifications and their key roles, and contributed to novel discoveries. This review article discusses recently published developments in separation and identification of bioactive proteins/peptides from milk and milk EVs, including MS-based proteomic approaches.
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Affiliation(s)
- Miroslava Stastna
- Institute of Analytical Chemistry of the Czech Academy of Sciences, Brno, Czech Republic
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23
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André-Grégoire G, Roux Q, Gavard J. Isolating plasma extracellular vesicles from mouse blood using size-exclusion chromatography, density gradient, and ultracentrifugation. STAR Protoc 2023; 4:102740. [PMID: 38048217 PMCID: PMC10746516 DOI: 10.1016/j.xpro.2023.102740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 10/16/2023] [Accepted: 11/09/2023] [Indexed: 12/06/2023] Open
Abstract
Circulating extracellular vesicles (EVs) could serve for the surveillance of diverse pathological conditions. We present a protocol for enriching and isolating plasma EVs from mouse blood. We describe steps for employing ultracentrifugation, size-exclusion chromatography, and density gradients, required for further quantitative and qualitative analysis. We detail the procedure for retrieving optimal volume of blood while preserving its integrity and avoiding hemolysis. We also describe the preparation of EVs from this complex fluid containing soluble proteins, aggregates, and lipoprotein particles. For complete details on the use and execution of this protocol, please refer to André-Grégoire et al. (2022).1.
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Affiliation(s)
- Gwennan André-Grégoire
- Team SOAP, CRCI2NA, Nantes Université, Inserm, CNRS, Université d'Angers, 44000 Nantes, France; Equipe Labellisée Ligue Nationale Contre le Cancer, 75013 Paris, France; Institut de Cancérologie de l'Ouest (ICO), 44800 Saint-Herblain, France.
| | - Quentin Roux
- Team SOAP, CRCI2NA, Nantes Université, Inserm, CNRS, Université d'Angers, 44000 Nantes, France; Equipe Labellisée Ligue Nationale Contre le Cancer, 75013 Paris, France.
| | - Julie Gavard
- Team SOAP, CRCI2NA, Nantes Université, Inserm, CNRS, Université d'Angers, 44000 Nantes, France; Equipe Labellisée Ligue Nationale Contre le Cancer, 75013 Paris, France; Institut de Cancérologie de l'Ouest (ICO), 44800 Saint-Herblain, France.
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24
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Lee S, Verkhoturov DS, Eller MJ, Verkhoturov SV, Shaw MA, Gwon K, Kim Y, Lucien F, Malhi H, Revzin A, Schweikert EA. Nanoprojectile Secondary Ion Mass Spectrometry Enables Multiplexed Analysis of Individual Hepatic Extracellular Vesicles. ACS Nano 2023; 17:23584-23594. [PMID: 38033295 PMCID: PMC10985841 DOI: 10.1021/acsnano.3c06604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2023]
Abstract
Extracellular vesicles (EVs) are nanoscale lipid bilayer particles secreted by cells. EVs may carry markers of the tissue of origin and its disease state, which makes them incredibly promising for disease diagnosis and surveillance. While the armamentarium of EV analysis technologies is rapidly expanding, there remains a strong need for multiparametric analysis with single EV resolution. Nanoprojectile (NP) secondary ion mass spectrometry (NP-SIMS) relies on bombarding a substrate of interest with individual gold NPs resolved in time and space. Each projectile creates an impact crater of 10-20 nm in diameter while molecules emitted from each impact are mass analyzed and recorded as individual mass spectra. We demonstrate the utility of NP-SIMS for statistical analysis of single EVs derived from normal liver cells (hepatocytes) and liver cancer cells. EVs were captured on antibody (Ab)-functionalized gold substrate and then labeled with Abs carrying lanthanide (Ln) MS tags (Ab@Ln). These tags targeted four markers selected for identifying all EVs, and specific to hepatocytes or liver cancer. NP-SIMS was used to detect Ab@Ln-tags colocalized on the same EV and to construct scatter plots of surface marker expression for thousands of EVs with the capability of categorizing individual EVs. Additionally, NP-SIMS revealed information about the chemical nanoenvironment where targeted moieties colocalized. Our approach allowed analysis of population heterogeneity with single EV resolution and distinguishing between hepatocyte and liver cancer EVs based on surface marker expression. NP-SIMS holds considerable promise for multiplexed analysis of single EVs and may become a valuable tool for identifying and validating EV biomarkers of cancer and other diseases.
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Affiliation(s)
- Seonhwa Lee
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, 55905, USA
| | | | - Michael J. Eller
- Department of Chemistry and Biochemistry, California State University Northridge, Northridge, CA 91330, USA
| | | | - Michael A. Shaw
- Department of Chemistry and Biochemistry, California State University Northridge, Northridge, CA 91330, USA
| | - Kihak Gwon
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, 55905, USA
| | - Yohan Kim
- Departments of Urology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Fabrice Lucien
- Departments of Urology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Harmeet Malhi
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Alexander Revzin
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, 55905, USA
| | - Emile A. Schweikert
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, USA
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25
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Abyadeh M, Alikhani M, Mirzaei M, Gupta V, Shekari F, Salekdeh GH. Proteomics provides insights into the theranostic potential of extracellular vesicles. Adv Protein Chem Struct Biol 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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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
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26
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Chang K, Fang Y, He P, Zhu C, Liu X, Zheng D, Chen D, Liu C. Employing the Anchor DSPE-PEG as a Redox Probe for Ratiometric Electrochemical Detection of Surface Proteins on Extracellular Vesicles with Aptamers. Anal Chem 2023; 95:16194-16200. [PMID: 37889159 DOI: 10.1021/acs.analchem.3c02948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
Quantitative analysis of surface proteins on extracellular vesicles (EVs) has been considered to be a crucial approach for reflecting the status of diseases. Due to the diverse composition of surface proteins on EVs and the interference from nonvesicular proteins, accurately detecting the expression of surface proteins on EVs remains a challenging task. While membrane affinity molecules have been widely employed as EVs capture probes to address this issue, their inherent biochemical properties have not been effectively harnessed. In this paper, we found that the electrochemical redox activity of the DSPE-PEG molecule was diminished upon its insertion into the membrane of EVs. This observation establishes the DSPE-PEG molecule modified on the Au electrode surface as a capture and a redox probe for the electrochemical detection of EVs. By utilizing methylene blue-labeled aptamers, the targeted surface proteins of EVs can be detected by recording the ratio of the oxidation peak current of methylene blue and DSPE-PEG. Without complicated signal amplification, the detection limit for EVs is calculated to be 8.11 × 102 particles/mL. Using this platform, we directly analyzed the expression of CD63 and HER2 proteins on the surface of EVs in human clinical plasma samples, demonstrating its significant potential in distinguishing breast cancer patients from healthy individuals.
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Affiliation(s)
- Kaili Chang
- The Key Laboratory of Cognitive Science of State Ethnic Affairs Commission, Hubei Key Laboratory of Medical Information Analysis and Tumor Diagnosis and Treatment, College of Biomedical Engineering, South-Central Minzu University, Wuhan 430074, China
| | - Yi Fang
- The Key Laboratory of Cognitive Science of State Ethnic Affairs Commission, Hubei Key Laboratory of Medical Information Analysis and Tumor Diagnosis and Treatment, College of Biomedical Engineering, South-Central Minzu University, Wuhan 430074, China
| | - Ping He
- The Key Laboratory of Cognitive Science of State Ethnic Affairs Commission, Hubei Key Laboratory of Medical Information Analysis and Tumor Diagnosis and Treatment, College of Biomedical Engineering, South-Central Minzu University, Wuhan 430074, China
| | - Chunnan Zhu
- The Key Laboratory of Cognitive Science of State Ethnic Affairs Commission, Hubei Key Laboratory of Medical Information Analysis and Tumor Diagnosis and Treatment, College of Biomedical Engineering, South-Central Minzu University, Wuhan 430074, China
| | - Xiaojun Liu
- The Key Laboratory of Cognitive Science of State Ethnic Affairs Commission, Hubei Key Laboratory of Medical Information Analysis and Tumor Diagnosis and Treatment, College of Biomedical Engineering, South-Central Minzu University, Wuhan 430074, China
| | - Dongyun Zheng
- The Key Laboratory of Cognitive Science of State Ethnic Affairs Commission, Hubei Key Laboratory of Medical Information Analysis and Tumor Diagnosis and Treatment, College of Biomedical Engineering, South-Central Minzu University, Wuhan 430074, China
| | - Dongjuan Chen
- Department of Laboratory Medicine, Maternal and Child Health Hospital of Hubei Province, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430070, China
| | - Chao Liu
- The Key Laboratory of Cognitive Science of State Ethnic Affairs Commission, Hubei Key Laboratory of Medical Information Analysis and Tumor Diagnosis and Treatment, College of Biomedical Engineering, South-Central Minzu University, Wuhan 430074, China
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27
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Qin T, Li P, Li J, Guo Q, Chen Y, Wang YE, Tao L, Huang J, Shen X, Wu X. Size-exclusion chromatography-based extracellular vesicle size subtyping and multiplex membrane protein profiling for differentiating gastrointestinal cancer prognosis. Analyst 2023; 148:5745-5752. [PMID: 37842723 DOI: 10.1039/d3an01027a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2023]
Abstract
Extracellular vesicles (EVs), as a type of subcellular structure, have been extensively researched for their potential for developing advanced diagnostic technologies for various diseases. However, the biomolecular and biophysical heterogeneity of EVs has restricted their application in clinical settings. In this article, we developed a size-exclusion chromatography-based technique for simultaneous EV size subtyping and protein profiling. By eluting fluorescent aptamer-treated patient plasma through a size-exclusion column, the mixture can be classified into 50 nm aptamer-bound EVs, 100 nm aptamer-bound EVs and free-floating aptamers, which could further enable multiplex EV membrane protein profiling by analyzing the fluorescence intensities of EV-bound aptamers. Using this technique, we successfully identified EV size subtypes for differentiating gastrointestinal cancer prognosis states. Overall, we developed a rapid, user-friendly and low-cost EV size subtyping and protein profiling technique, which holds great potential for identifying crucial EV size subtypes for disease diagnosis in the clinic.
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Affiliation(s)
- Ti Qin
- State Key Laboratory of Functions and Applications of Medicinal Plants, School of Pharmaceutical Sciences, Guizhou Medical University, University Town, Guian New District, 550025, Guizhou, China.
- The High Efficacy Application of Natural Medicinal Resources Engineering Center of Guizhou Province, School of Pharmaceutical Sciences, Guizhou Medical University, University Town, Guian New District, 550025, Guizhou, China
| | - Pinhao Li
- Department of Pathology, The Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Jun Li
- Hongkong Well Hope Group Limited, 6/F RFCM, Manulife Place.348 Kwun Tong Road, Kowloon, 999077, Hong Kong, China
| | - Qianqian Guo
- State Key Laboratory of Functions and Applications of Medicinal Plants, School of Pharmaceutical Sciences, Guizhou Medical University, University Town, Guian New District, 550025, Guizhou, China.
- The High Efficacy Application of Natural Medicinal Resources Engineering Center of Guizhou Province, School of Pharmaceutical Sciences, Guizhou Medical University, University Town, Guian New District, 550025, Guizhou, China
| | - Ying Chen
- State Key Laboratory of Functions and Applications of Medicinal Plants, School of Pharmaceutical Sciences, Guizhou Medical University, University Town, Guian New District, 550025, Guizhou, China.
- The High Efficacy Application of Natural Medicinal Resources Engineering Center of Guizhou Province, School of Pharmaceutical Sciences, Guizhou Medical University, University Town, Guian New District, 550025, Guizhou, China
| | - Yu-E Wang
- State Key Laboratory of Functions and Applications of Medicinal Plants, School of Pharmaceutical Sciences, Guizhou Medical University, University Town, Guian New District, 550025, Guizhou, China.
- The High Efficacy Application of Natural Medicinal Resources Engineering Center of Guizhou Province, School of Pharmaceutical Sciences, Guizhou Medical University, University Town, Guian New District, 550025, Guizhou, China
| | - Ling Tao
- State Key Laboratory of Functions and Applications of Medicinal Plants, School of Pharmaceutical Sciences, Guizhou Medical University, University Town, Guian New District, 550025, Guizhou, China.
- The High Efficacy Application of Natural Medicinal Resources Engineering Center of Guizhou Province, School of Pharmaceutical Sciences, Guizhou Medical University, University Town, Guian New District, 550025, Guizhou, China
| | - Jian Huang
- Center for Clinical Laboratories, The Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, Guizhou, China.
- School of Clinical Laboratory Science, Guizhou Medical University, University Town, Guian New District, 550025, Guizhou, China
| | - Xiangchun Shen
- State Key Laboratory of Functions and Applications of Medicinal Plants, School of Pharmaceutical Sciences, Guizhou Medical University, University Town, Guian New District, 550025, Guizhou, China.
- The High Efficacy Application of Natural Medicinal Resources Engineering Center of Guizhou Province, School of Pharmaceutical Sciences, Guizhou Medical University, University Town, Guian New District, 550025, Guizhou, China
| | - Xingjie Wu
- State Key Laboratory of Functions and Applications of Medicinal Plants, School of Pharmaceutical Sciences, Guizhou Medical University, University Town, Guian New District, 550025, Guizhou, China.
- The High Efficacy Application of Natural Medicinal Resources Engineering Center of Guizhou Province, School of Pharmaceutical Sciences, Guizhou Medical University, University Town, Guian New District, 550025, Guizhou, China
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28
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Darragh IAJ, McNamee N, Daly R, Pacheco SM, O'Driscoll L, Egan B. The separation and identification of circulating small extracellular vesicles from endurance-trained, strength-trained and recreationally active men. J Physiol 2023; 601:5075-5091. [PMID: 37725436 DOI: 10.1113/jp285170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 08/30/2023] [Indexed: 09/21/2023] Open
Abstract
Small extracellular vesicles (EV) are membrane-encapsulated particles that carry bioactive cargoes, are released by all cell types and are present in all human biofluids. Changes in EV profiles and abundance occur in response to acute exercise, but this study investigated whether individuals with divergent histories of exercise training (recreationally active controls - CON; endurance-trained - END; strength-trained - STR) presented with varied abundances of small EVs in resting samples and whether the abundance of small EVs differed within each group across two measurement days. Participants (n = 38, all male; CON n = 12, END n = 13, STR n = 13) arrived at the lab on two separate occasions in a rested, overnight fasted state, with standardisation of time of day of sampling, recent dietary intake, time since last meal and time since last exercise training session (∼40 h). Whole blood samples were collected and separated into plasma from which small EVs were separated using size exclusion chromatography and identified in accordance with the Minimal Information For Studies of Extracellular Vesicles (MISEV) guidelines. No differences in the abundance of small EVs were observed within or between groups across multiple methods of small EV identification (nanoparticle tracking analysis, flow cytometry, immunoblot of specific EV markers). Targeted metabolomics of the small EV preparations identified 96 metabolites that were associated with the structure and function of small EVs, with no statistically significant differences in concentrations observed across groups. The results of the current study suggest that the abundance and metabolomic profile of small EVs derived from men with divergent histories of exercise training are similar to those in resting blood samples. KEY POINTS: Extracellular vesicles (EV) are membrane-encapsulated particles that are present in circulation and carry bioactive materials as 'cargo'. The abundance and profile of small EVs are responsive to acute exercise, but little is known about the relationship between small EVs and exercise training. This study examined the abundance, and a targeted metabolomic profile, of small EVs separated from the blood of endurance athletes, strength athletes and recreationally active controls at rest (∼40 h after the most recent exercise session) on two separate but identical lab visits. No differences were observed in the abundance or metabolomic profile of small EV preparations between the groups or between the lab visits within each group. Further research should determine whether the bioactive cargoes (e.g. RNA, protein and additional metabolites) carried within EVs are altered in individuals with divergent histories of exercise training or in response to exercise training interventions.
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Affiliation(s)
- Ian A J Darragh
- School of Health and Human Performance, Dublin City University, Dublin, Ireland
| | - Niamh McNamee
- School of Pharmacy and Pharmaceutical Sciences, Trinity College Dublin, Dublin, Ireland
- Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
- Trinity St. James's Cancer Institute, Trinity College Dublin, Dublin, Ireland
| | - Róisín Daly
- School of Pharmacy and Pharmaceutical Sciences, Trinity College Dublin, Dublin, Ireland
- Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
- Trinity St. James's Cancer Institute, Trinity College Dublin, Dublin, Ireland
| | - Sarai Martinez Pacheco
- School of Pharmacy and Pharmaceutical Sciences, Trinity College Dublin, Dublin, Ireland
- Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
- Trinity St. James's Cancer Institute, Trinity College Dublin, Dublin, Ireland
| | - Lorraine O'Driscoll
- School of Pharmacy and Pharmaceutical Sciences, Trinity College Dublin, Dublin, Ireland
- Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
- Trinity St. James's Cancer Institute, Trinity College Dublin, Dublin, Ireland
| | - Brendan Egan
- School of Health and Human Performance, Dublin City University, Dublin, Ireland
- Florida Institute for Human and Machine Cognition, Pensacola, Florida, USA
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Lucchetti D, Colella F, Artemi G, Haque S, Sgambato A, Pellicano R, Fagoonee S. Smart nano-sized extracellular vesicles for cancer therapy: Potential theranostic applications in gastrointestinal tumors. Crit Rev Oncol Hematol 2023; 191:104121. [PMID: 37690633 DOI: 10.1016/j.critrevonc.2023.104121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 01/27/2023] [Accepted: 09/04/2023] [Indexed: 09/12/2023] Open
Abstract
Extracellular vesicles (EVs) have gained tremendous interest in the search for next-generation therapeutics for the treatment of a range of pathologies, including cancer, especially due to their small size, biomolecular cargo, ability to mediate intercellular communication, high physicochemical stability, low immunogenicity and biocompatibility. The theranostic potential of EVs have been enhanced by adopting several strategies such as genetic or metabolic engineering, parental cell modification or direct functionalization to incorporate therapeutic compounds into these nanoplatforms. The smart nano-sized EVs indeed offer huge opportunities in the field of cancer, and current research is set at overcoming the existing pitfalls. Smart EVs are already being applied in the clinics despite the challenges faced. We provide, herein, an update on the technologies employed for EV functionalization in order to achieve optimal tumor cell targeting and EV tracking in vivo with bio-imaging modalities, as well as the preclinical and clinical studies making use of these modified EVs, in the context of gastrointestinal tumors.
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Affiliation(s)
- Donatella Lucchetti
- Fondazione Policlinico Universitario 'Agostino Gemelli' IRCCS, Rome, Italy; Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Filomena Colella
- Fondazione Policlinico Universitario 'Agostino Gemelli' IRCCS, Rome, Italy
| | - Giulia Artemi
- Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan 45142, Saudi Arabia; Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut 1102 2801, Lebanon; Centre of Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman 13306, United Arab Emirates
| | - Alessandro Sgambato
- Fondazione Policlinico Universitario 'Agostino Gemelli' IRCCS, Rome, Italy; Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, Rome, Italy.
| | - Rinaldo Pellicano
- Gastroenterology Unit, Città della salute e della Scienza Hospital, Turin, Italy
| | - Sharmila Fagoonee
- Institute of Biostructure and Bioimaging (CNR), Molecular Biotechnology Center, Turin, Italy
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van Maanen JC, Bach FC, Braun TS, Giovanazzi A, van Balkom BW, Templin M, Wauben MH, Tryfonidou MA. A Combined Western and Bead-Based Multiplex Platform to Characterize Extracellular Vesicles. Tissue Eng Part C Methods 2023; 29:493-504. [PMID: 37470213 PMCID: PMC10654656 DOI: 10.1089/ten.tec.2023.0056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 06/21/2023] [Indexed: 07/21/2023] Open
Abstract
In regenerative medicine, extracellular vesicles (EVs) are considered as a promising cell-free approach. EVs are lipid bilayer-enclosed vesicles secreted by cells and are key players in intercellular communication. EV-based therapeutic approaches have unique advantages over the use of cell-based therapies, such as a high biological, but low immunogenic and tumorigenic potential. To analyze the purity and biochemical composition of EV preparations, the International Society for Extracellular Vesicles (ISEV) has prepared guidelines recommending the analysis of multiple (EV) markers, as well as proteins coisolated/recovered with EVs. Traditional methods for EV characterization, such as Western blotting, require a relatively high EV sample/protein input for the analysis of one protein. We here evaluate a combined Western and bead-based multiplex platform, called DigiWest, for its ability to detect simultaneously multiple EV markers in an EV-containing sample with inherent low protein input. DigiWest analysis was performed on EVs from various sources and species, including mesenchymal stromal cells, notochordal cells, and milk, from human, pig, and dog. The study established a panel of nine antibodies that can be used as cross-species for the detection of general EV markers and coisolates in accordance with the ISEV guidelines. This optimized panel facilitates the parallel evaluation of EV-containing samples, allowing for a comprehensive characterization and assessment of their purity. The total protein input for marker analysis with DigiWest was 1 μg for all nine antibodies, compared with ∼10 μg protein input required for traditional Western blotting for one antibody. These findings demonstrate the potential of the DigiWest technique for characterizing various types of EVs in the regenerative medicine field.
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Affiliation(s)
- Josette C. van Maanen
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Frances C. Bach
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Theresa S. Braun
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Alberta Giovanazzi
- Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Bas W.M. van Balkom
- Department of Nephrology and Hypertension, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Markus Templin
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
- NMI TT Pharmaservices, Berlin, Germany
| | - Marca H.M. Wauben
- Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Marianna A. Tryfonidou
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
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31
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Lee ZC, Hadisurya M, Luo Z, Li L, Tao WA. Hands-Free Proteomic Profiling of Urinary Extracellular Vesicles with a High-Throughput Automated Workflow. J Am Soc Mass Spectrom 2023; 34:2585-2593. [PMID: 37870912 DOI: 10.1021/jasms.3c00329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2023]
Abstract
Extracellular vesicles (EVs) have emerged as a promising source of disease biomarkers for noninvasive early stage diagnoses, but a bottleneck in EV sample processing restricts their immense potential in clinical applications. Existing methods are limited by a low EV yield and integrity, slow processing speeds, low sample capacity, and poor recovery efficiency. We aimed to address these issues with a high-throughput automated workflow for EV isolation, EV lysis, protein extraction, and protein denaturation. The automation can process clinical urine samples in parallel, resulting in protein-covered beads ready for various analytical methods, including immunoassays, protein quantitation assays, and mass spectrometry. Compared to the standard manual lysis method for contamination levels, efficiency, and consistency of EV isolation, the automated protocol shows reproducible and robust proteomic quantitation with less than a 10% median coefficient of variation. When we applied the method to clinical samples, we identified a total 3,793 unique proteins and 40,380 unique peptides, with 992 significantly upregulated proteins in kidney cancer patients versus healthy controls. These upregulated proteins were found to be involved in several important kidney cancer metabolic pathways also identified with a manual control. This hands-free workflow represents a practical EV extraction and profiling approach that can benefit both clinical and research applications, streamlining biomarker discovery, tumor monitoring, and early cancer diagnoses.
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Affiliation(s)
- Zheng-Chi Lee
- West Lafayette Junior/Senior High School, West Lafayette, Indiana 47906, United States
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Marco Hadisurya
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Zhuojun Luo
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Li Li
- Tymora Analytical Operations, West Lafayette, Indiana 47906, United States
| | - W Andy Tao
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, United States
- Tymora Analytical Operations, West Lafayette, Indiana 47906, United States
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
- Purdue Institute for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
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32
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Liu YK, Wu X, Hadisurya M, Li L, Kaimakliotis H, Iliuk A, Tao WA. One-Pot Analytical Pipeline for Efficient and Sensitive Proteomic Analysis of Extracellular Vesicles. J Proteome Res 2023; 22:3301-3310. [PMID: 37702715 PMCID: PMC10897859 DOI: 10.1021/acs.jproteome.3c00361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/14/2023]
Abstract
Extracellular vesicle (EV) proteomics emerges as an effective tool for discovering potential biomarkers for disease diagnosis, monitoring, and therapeutics. However, the current workflow of mass spectrometry-based EV proteome analysis is not fully compatible in a clinical setting due to inefficient EV isolation methods and a tedious sample preparation process. To streamline and improve the efficiency of EV proteome analysis, here we introduce a one-pot analytical pipeline integrating a robust EV isolation approach, EV total recovery and purification (EVtrap), with in situ protein sample preparation, to detect urinary EV proteome. By incorporating solvent-driven protein capture and fast on-bead digestion, the one-pot pipeline enabled the whole EV proteome analysis to be completed within one day. In comparison with the existing workflow, the one-pot pipeline was able to obtain better peptide yield and identify the equivalent number of unique EV proteins from 1 mL of urine. Finally, we applied the one-pot pipeline to profile proteomes in urinary EVs of bladder cancer patients. A total of 2774 unique proteins were identified in 53 urine samples using a 15 min gradient library-free data-independent acquisition method. Taken altogether, our novel one-pot analytical pipeline demonstrated its potential for routine and robust EV proteomics in biomedical applications.
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Affiliation(s)
- Yi-Kai Liu
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Xiaofeng Wu
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Marco Hadisurya
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Li Li
- Tymora Analytical Operations, West Lafayette, Indiana 47906, United States
| | - Hristos Kaimakliotis
- Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
| | - Anton Iliuk
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, United States
- Tymora Analytical Operations, West Lafayette, Indiana 47906, United States
| | - W Andy Tao
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, United States
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
- Tymora Analytical Operations, West Lafayette, Indiana 47906, United States
- Purdue Institute for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
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33
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Kang J, Mun D, Chun Y, Park D, Kim H, Yun N, Joung B. Engineered small extracellular vesicle-mediated NOX4 siRNA delivery for targeted therapy of cardiac hypertrophy. J Extracell Vesicles 2023; 12:e12371. [PMID: 37795828 PMCID: PMC10552075 DOI: 10.1002/jev2.12371] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 09/18/2023] [Accepted: 09/27/2023] [Indexed: 10/06/2023] Open
Abstract
Small-interfering RNA (siRNA) therapy is considered a powerful therapeutic strategy for treating cardiac hypertrophy, an important risk factor for subsequent cardiac morbidity and mortality. However, the lack of safe and efficient in vivo delivery of siRNAs is a major challenge for broadening its clinical applications. Small extracellular vesicles (sEVs) are a promising delivery system for siRNAs but have limited cell/tissue-specific targeting ability. In this study, a new generation of heart-targeting sEVs (CEVs) has been developed by conjugating cardiac-targeting peptide (CTP) to human peripheral blood-derived sEVs (PB-EVs), using a simple, rapid and scalable method based on bio-orthogonal copper-free click chemistry. The experimental results show that CEVs have typical sEVs properties and excellent heart-targeting ability. Furthermore, to treat cardiac hypertrophy, CEVs are loaded with NADPH Oxidase 4 (NOX4) siRNA (siNOX4). Consequently, CEVs@siNOX4 treatment enhances the in vitro anti-hypertrophic effects by CEVs with siRNA protection and heart-targeting ability. In addition, the intravenous injection of CEVs@siNOX4 into angiotensin II (Ang II)-treated mice significantly improves cardiac function and reduces fibrosis and cardiomyocyte cross-sectional area, with limited side effects. In conclusion, the utilization of CEVs represents an efficient strategy for heart-targeted delivery of therapeutic siRNAs and holds great promise for the treatment of cardiac hypertrophy.
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Affiliation(s)
- Ji‐Young Kang
- Division of Cardiology, Department of Internal MedicineYonsei University College of MedicineSeodaemun‐guSeoulRepublic of Korea
| | - Dasom Mun
- Division of Cardiology, Department of Internal MedicineYonsei University College of MedicineSeodaemun‐guSeoulRepublic of Korea
| | - Yumin Chun
- Division of Cardiology, Department of Internal MedicineYonsei University College of MedicineSeodaemun‐guSeoulRepublic of Korea
| | - Da‐Seul Park
- Division of Cardiology, Department of Internal MedicineYonsei University College of MedicineSeodaemun‐guSeoulRepublic of Korea
| | - Hyoeun Kim
- Department of Biochemistry and Molecular BiologyYonsei University College of MedicineSeodaemun‐guSeoulRepublic of Korea
| | - Nuri Yun
- GNTPharma Science and Technology Center for Health, Giheung‐guYongin‐siIncheonRepublic of Korea
| | - Boyoung Joung
- Division of Cardiology, Department of Internal MedicineYonsei University College of MedicineSeodaemun‐guSeoulRepublic of Korea
- Graduate School of Medical Science, Brain Korea 21 ProjectYonsei University College of MedicineSeodaemun‐guSeoulRepublic of Korea
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34
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Turner NP, Abeysinghe P, Sadowski P, Mitchell MD. Omics Analysis of Extracellular Vesicles Recovered from Infant Formula Products and Milk: Towards Personalized Infant Nutrition. Mol Nutr Food Res 2023; 67:e2300404. [PMID: 37562982 DOI: 10.1002/mnfr.202300404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/26/2023] [Indexed: 08/12/2023]
Abstract
SCOPE Milk and milk products such as infant formula (IF) play a fundamental role in serving the nutritional needs of the developing infant. Extracellular vesicles (EVs) in human (HM) and cow milk (CM) contain molecular cargo such as proteins and micro(mi)RNAs that serve as functional messengers between cells and may be of importance to infant health. Most IF is derived from a CM protein base, however differences between HM and CM EV molecular cargo have not been extensively studied. METHODS AND RESULTS This study develops a pipeline using advanced proteomics and transcriptomics to enable cross-species comparison of milk and IF EVs. The number of nanoparticles per mL of IF is significantly reduced compared to unprocessed CM. 130 proteins and 514 miRNAs are differentially abundant between HM and CM EVs. While 90% of CM EV miRNAs are also identified in IF EVs, only 20% of CM EV proteins are identified in IF EVs. CONCLUSIONS This workflow identifies key species-specific differences that can be used to optimize IF recipes and enhance infant nutrition. Improved preservation of EV functional molecular cargo in IF products is of critical importance to retaining molecular drivers of good health and should be the focus of future investigations.
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Affiliation(s)
- Natalie P Turner
- Centre for Children's Health Research (CCHR), Queensland University of Technology (QUT), 62 Graham Street, South Brisbane, QLD, 4101, Australia
| | - Pevindu Abeysinghe
- Centre for Children's Health Research (CCHR), Queensland University of Technology (QUT), 62 Graham Street, South Brisbane, QLD, 4101, Australia
| | - Pawel Sadowski
- Central Analytical Research Facility (CARF), QUT, Gardens Point Campus, 2 George Street, Brisbane City, QLD, 4000, Australia
| | - Murray D Mitchell
- Centre for Children's Health Research (CCHR), Queensland University of Technology (QUT), 62 Graham Street, South Brisbane, QLD, 4101, Australia
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35
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Ridolfi A, Conti L, Brucale M, Frigerio R, Cardellini J, Musicò A, Romano M, Zendrini A, Polito L, Bergamaschi G, Gori A, Montis C, Panella S, Barile L, Berti D, Radeghieri A, Bergese P, Cretich M, Valle F. Particle profiling of EV-lipoprotein mixtures by AFM nanomechanical imaging. J Extracell Vesicles 2023; 12:e12349. [PMID: 37855042 PMCID: PMC10585431 DOI: 10.1002/jev2.12349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 07/08/2023] [Indexed: 10/20/2023] Open
Abstract
The widely overlapping physicochemical properties of lipoproteins (LPs) and extracellular vesicles (EVs) represents one of the main obstacles for the isolation and characterization of these pervasive biogenic lipid nanoparticles. We herein present the application of an atomic force microscopy (AFM)-based quantitative morphometry assay to the rapid nanomechanical screening of mixed LPs and EVs samples. The method can determine the diameter and the mechanical stiffness of hundreds of individual nanometric objects within few hours. The obtained diameters are in quantitative accord with those measured via cryo-electron microscopy (cryo-EM); the assignment of specific nanomechanical readout to each object enables the simultaneous discrimination of co-isolated EVs and LPs even if they have overlapping size distributions. EVs and all classes of LPs are shown to be characterised by specific combinations of diameter and stiffness, thus making it possible to estimate their relative abundance in EV/LP mixed samples in terms of stoichiometric ratio, surface area and volume. As a side finding, we show how the mechanical behaviour of specific LP classes is correlated to distinctive structural features revealed by cryo-EM. The described approach is label-free, single-step and relatively quick to perform. Importantly, it can be used to analyse samples which prove very challenging to assess with several established techniques due to ensemble-averaging, low sensibility to small particles, or both, thus providing a very useful tool for quickly assessing the purity of EV/LP isolates including plasma- and serum-derived preparations.
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Affiliation(s)
- Andrea Ridolfi
- Consiglio Nazionale delle RicercheIstituto per lo Studio dei Materiali NanostrutturatiBolognaItaly
| | - Laura Conti
- Consiglio Nazionale delle RicercheIstituto per lo Studio dei Materiali NanostrutturatiBolognaItaly
| | - Marco Brucale
- Consiglio Nazionale delle RicercheIstituto per lo Studio dei Materiali NanostrutturatiBolognaItaly
- Consorzio Interuniversitario per lo Sviluppo dei Sistemi a Grande InterfaseFirenzeItaly
| | - Roberto Frigerio
- Consiglio Nazionale delle RicercheIstituto di Scienze e Tecnologie Chimiche “Giulio Natta”MilanItaly
- Dipartimento di Medicina Molecolare e TraslazionaleUniversità degli Studi di BresciaBresciaItaly
| | - Jacopo Cardellini
- Dipartimento di Chimica “Ugo Schiff”Università degli Studi di FirenzeFirenzeItaly
| | - Angelo Musicò
- Consorzio Interuniversitario per lo Sviluppo dei Sistemi a Grande InterfaseFirenzeItaly
- Consiglio Nazionale delle RicercheIstituto di Scienze e Tecnologie Chimiche “Giulio Natta”MilanItaly
- Dipartimento di Medicina Molecolare e TraslazionaleUniversità degli Studi di BresciaBresciaItaly
| | - Miriam Romano
- Consorzio Interuniversitario per lo Sviluppo dei Sistemi a Grande InterfaseFirenzeItaly
- Dipartimento di Medicina Molecolare e TraslazionaleUniversità degli Studi di BresciaBresciaItaly
| | - Andrea Zendrini
- Consorzio Interuniversitario per lo Sviluppo dei Sistemi a Grande InterfaseFirenzeItaly
- Dipartimento di Medicina Molecolare e TraslazionaleUniversità degli Studi di BresciaBresciaItaly
| | - Laura Polito
- Consiglio Nazionale delle RicercheIstituto di Scienze e Tecnologie Chimiche “Giulio Natta”MilanItaly
| | - Greta Bergamaschi
- Consiglio Nazionale delle RicercheIstituto di Scienze e Tecnologie Chimiche “Giulio Natta”MilanItaly
| | - Alessandro Gori
- Consiglio Nazionale delle RicercheIstituto di Scienze e Tecnologie Chimiche “Giulio Natta”MilanItaly
| | - Costanza Montis
- Consorzio Interuniversitario per lo Sviluppo dei Sistemi a Grande InterfaseFirenzeItaly
- Dipartimento di Chimica “Ugo Schiff”Università degli Studi di FirenzeFirenzeItaly
| | - Stefano Panella
- Istituto Cardiocentro TicinoEnte Ospedaliero CantonaleLuganoSwitzerland
| | - Lucio Barile
- Istituto Cardiocentro TicinoEnte Ospedaliero CantonaleLuganoSwitzerland
| | - Debora Berti
- Consorzio Interuniversitario per lo Sviluppo dei Sistemi a Grande InterfaseFirenzeItaly
- Dipartimento di Chimica “Ugo Schiff”Università degli Studi di FirenzeFirenzeItaly
| | - Annalisa Radeghieri
- Consorzio Interuniversitario per lo Sviluppo dei Sistemi a Grande InterfaseFirenzeItaly
- Dipartimento di Medicina Molecolare e TraslazionaleUniversità degli Studi di BresciaBresciaItaly
| | - Paolo Bergese
- Consorzio Interuniversitario per lo Sviluppo dei Sistemi a Grande InterfaseFirenzeItaly
- Dipartimento di Medicina Molecolare e TraslazionaleUniversità degli Studi di BresciaBresciaItaly
- Consiglio Nazionale delle Ricerche, Istituto per la Ricerca e l'innovazione BiomedicaPalermoItaly
| | - Marina Cretich
- Consiglio Nazionale delle RicercheIstituto di Scienze e Tecnologie Chimiche “Giulio Natta”MilanItaly
| | - Francesco Valle
- Consiglio Nazionale delle RicercheIstituto per lo Studio dei Materiali NanostrutturatiBolognaItaly
- Consorzio Interuniversitario per lo Sviluppo dei Sistemi a Grande InterfaseFirenzeItaly
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36
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Saari H, Pusa R, Marttila H, Yliperttula M, Laitinen S. Development of tandem cation exchange chromatography for high purity extracellular vesicle isolation: The effect of ligand steric availability. J Chromatogr A 2023; 1707:464293. [PMID: 37579702 DOI: 10.1016/j.chroma.2023.464293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 08/07/2023] [Accepted: 08/08/2023] [Indexed: 08/16/2023]
Abstract
Purification of extracellular vesicles for research and therapeutic applications requires updated methodology to address the limitations of traditional ultracentrifugation and other size-based separation techniques. Their downfalls include induced extracellular vesicle aggregation, low yields, poor scalability and one-dimensionality of the separation process, as the size or sedimentation speed of extracellular vesicles is often the only selection criterion. Ion exchange chromatography is a promising alternative or supplementary method candidate, as it offers a different approach for extracellular vesicle separation, which is surface charge. For now, mostly anion exchange chromatography has been evaluated for extracellular vesicle purification, as it successfully relies on the strongly negative surface charge of extracellular vesicles. However, as extracellular vesicles are very complex in their structure, also cation exchange chromatography could be applicable, due to individual cationic domains on the extracellular vesicle surface. Here, we compare anion exchange chromatography to different types of cation exchange chromatography for the purification of platelet extracellular vesicle samples also containing plasma-derived impurities. We found that the choice of resin structure used for cation exchange chromatography is critical for binding platelet extracellular vesicles, as a conventional-type cation exchanger was found to only capture and elute less than 20% of extracellular vesicles. With the tentacle-type resin, it was possible to obtain comparable platelet extracellular vesicle yields (over 90%) with cation exchange chromatography compared to anion exchange chromatography, as well as superior purity, especially when it was combined to conventional cation exchange resin.
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Affiliation(s)
- Heikki Saari
- Finnish Red Cross Blood Service. Härkälenkki 13, 01730 Vantaa, Finland.
| | - Reetta Pusa
- Finnish Red Cross Blood Service. Härkälenkki 13, 01730 Vantaa, Finland
| | - Heli Marttila
- Molecular and Integrative Biosciences Research Programme, Biological and Environmental Sciences, University of Helsinki, Viikinkaari 9, 00790 Helsinki, Finland
| | - Marjo Yliperttula
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Viikinkaari 5, 00790 Helsinki, Finland
| | - Saara Laitinen
- Finnish Red Cross Blood Service. Härkälenkki 13, 01730 Vantaa, Finland
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37
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Lattmann E, Lapaire V, Levesque MP. Isolation and detection of extracellular vesicles from melanoma cells and liquid biopsies using size-exclusion chromatography and nano-flow cytometry. STAR Protoc 2023; 4:102365. [PMID: 37421613 PMCID: PMC10339257 DOI: 10.1016/j.xpro.2023.102365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 04/18/2023] [Accepted: 05/18/2023] [Indexed: 07/10/2023] Open
Abstract
Characterization of extracellular vesicles (EVs) holds great promise for biomarker discovery and understanding of diseases, including melanoma, the deadliest skin cancer type. Here, we describe a size-exclusion chromatography method to isolate and concentrate EVs from patient material including (1) patient-derived melanoma cell line supernatants and (2) plasma and serum biopsies. Additionally, we provide a protocol to analyze EVs by nano-flow cytometry. EV suspensions obtained with the presented protocol can be used for several downstream analyses including RNA sequencing and proteomics.
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Affiliation(s)
- Evelyn Lattmann
- Department of Dermatology, University of Zurich, University Hospital Zurich, Schlieren, ZH 8952, Switzerland.
| | - Valérie Lapaire
- Department of Dermatology, University of Zurich, University Hospital Zurich, Schlieren, ZH 8952, Switzerland
| | - Mitchell P Levesque
- Department of Dermatology, University of Zurich, University Hospital Zurich, Schlieren, ZH 8952, Switzerland.
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38
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Hao PC, Burnouf T, Chiang CW, Jheng PR, Szunerits S, Yang JC, Chuang EY. Enhanced diabetic wound healing using platelet-derived extracellular vesicles and reduced graphene oxide in polymer-coordinated hydrogels. J Nanobiotechnology 2023; 21:318. [PMID: 37667248 PMCID: PMC10478311 DOI: 10.1186/s12951-023-02068-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 08/17/2023] [Indexed: 09/06/2023] Open
Abstract
Impaired wound healing is a significant complication of diabetes. Platelet-derived extracellular vesicles (pEVs), rich in growth factors and cytokines, show promise as a powerful biotherapy to modulate cellular proliferation, angiogenesis, immunomodulation, and inflammation. For practical home-based wound therapy, however, pEVs should be incorporated into wound bandages with careful attention to delivery strategies. In this work, a gelatin-alginate hydrogel (GelAlg) loaded with reduced graphene oxide (rGO) was fabricated, and its potential as a diabetic wound dressing was investigated. The GelAlg@rGO-pEV gel exhibited excellent mechanical stability and biocompatibility in vitro, with promising macrophage polarization and reactive oxygen species (ROS)-scavenging capability. In vitro cell migration experiments were complemented by in vivo investigations using a streptozotocin-induced diabetic rat wound model. When exposed to near-infrared light at 2 W cm- 2, the GelAlg@rGO-pEV hydrogel effectively decreased the expression of inflammatory biomarkers, regulated immune response, promoted angiogenesis, and enhanced diabetic wound healing. Interestingly, the GelAlg@rGO-pEV hydrogel also increased the expression of heat shock proteins involved in cellular protective pathways. These findings suggest that the engineered GelAlg@rGO-pEV hydrogel has the potential to serve as a wound dressing that can modulate immune responses, inflammation, angiogenesis, and follicle regeneration in diabetic wounds, potentially leading to accelerated healing of chronic wounds.
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Affiliation(s)
- Ping-Chien Hao
- Graduate Institute of Biomedical Materials and Tissue Engineering, College of Biomedical Engineering, Taipei Medical University, Taipei, 11031, Taiwan
| | - Thierry Burnouf
- Graduate Institute of Biomedical Materials and Tissue Engineering, College of Biomedical Engineering, Taipei Medical University, Taipei, 11031, Taiwan
- International Ph.D. Program in Biomedical Engineering, College of Biomedical Engineering, Taipei Medical University, Taipei, 11031, Taiwan
| | - Chih-Wei Chiang
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, 10617, Taiwan
- Department of Orthopedics, Taipei Medical University Hospital, Taipei, 11031, Taiwan
| | - Pei-Ru Jheng
- Graduate Institute of Biomedical Materials and Tissue Engineering, College of Biomedical Engineering, Taipei Medical University, Taipei, 11031, Taiwan
| | - Sabine Szunerits
- Univ. Lille, CNRS, Centrale Lille, Univ. Polytechnique Hauts-de-France, UMR 8520, IEMN, Lille, F- 59000, France
| | - Jen-Chang Yang
- Graduate Institute of Nanomedicine and Medical Engineering, College of Biomedical Engineering, Taipei Medical University, Taipei, 110-52, Taiwan
| | - Er-Yuan Chuang
- Graduate Institute of Biomedical Materials and Tissue Engineering, College of Biomedical Engineering, Taipei Medical University, Taipei, 11031, Taiwan.
- International Ph.D. Program in Biomedical Engineering, College of Biomedical Engineering, Taipei Medical University, Taipei, 11031, Taiwan.
- Cell Physiology and Molecular Image Research Center, Taipei Medical University-Wan Fang Hospital, Taipei, 11696, Taiwan.
- Precision Medicine and Translational Cancer Research Center, Taipei Medical University Hospital, Taipei, 11031, Taiwan.
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Abbott A. FedEx for your cells: this biological delivery service could treat disease. Nature 2023; 621:462-464. [PMID: 37726444 DOI: 10.1038/d41586-023-02906-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/21/2023]
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40
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Normak K, Papp M, Ullmann M, Paganini C, Manno M, Bongiovanni A, Bergese P, Arosio P. Multiparametric Orthogonal Characterization of Extracellular Vesicles by Liquid Chromatography Combined with In-Line Light Scattering and Fluorescence Detection. Anal Chem 2023; 95:12443-12451. [PMID: 37556360 PMCID: PMC10448444 DOI: 10.1021/acs.analchem.3c02108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 07/27/2023] [Indexed: 08/11/2023]
Abstract
Extracellular vesicles (EVs) are membrane-enclosed biological nanoparticles with potential as diagnostic markers and carriers for therapeutics. Characterization of EVs poses severe challenges due to their complex structure and composition, requiring the combination of orthogonal analytical techniques. Here, we demonstrate how liquid chromatography combined with multi-angle light scattering (MALS) and fluorescence detection in one single apparatus can provide multiparametric characterization of EV samples, including concentration of particles, average diameter of the particles, protein amount to particle number ratio, presence of EV surface markers and lipids, EV shape, and sample purity. The method requires a small amount of sample of approximately 107 EVs, limited handling of the sample and data analysis time in the order of minutes; it is fully automatable and can be applied to both crude and purified samples.
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Affiliation(s)
- Karl Normak
- Department
of Chemistry and Applied Biosciences, ETH
Zurich, Zurich 8093, Switzerland
| | - Marcell Papp
- Department
of Chemistry and Applied Biosciences, ETH
Zurich, Zurich 8093, Switzerland
| | - Michael Ullmann
- Department
of Chemistry and Applied Biosciences, ETH
Zurich, Zurich 8093, Switzerland
| | - Carolina Paganini
- Department
of Chemistry and Applied Biosciences, ETH
Zurich, Zurich 8093, Switzerland
| | - Mauro Manno
- Institute
of Biophysics, National Research Council of Italy, Via Ugo la Malfa 153, Palermo 90146, Italy
| | - Antonella Bongiovanni
- Institute
for Research and Biomedical Innovation (IRIB), National Research Council
of Italy, Via Ugo La
Malfa 153, Palermo 90146, Italy
| | - Paolo Bergese
- Department
of Molecular and Translational Medicine, University of Brescia, Brescia 25123, Italy
- Center
for Colloid and Surface Science (CSGI), Florence 50019, Italy
| | - Paolo Arosio
- Department
of Chemistry and Applied Biosciences, ETH
Zurich, Zurich 8093, Switzerland
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41
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Bui TT, Jang E, Shin JH, Kim TH, Kim H, Choi D, Vu TD, Chung H. Feasibility of Raman spectroscopic identification of gall bladder cancer using extracellular vesicles extracted from bile. Analyst 2023; 148:4156-4165. [PMID: 37501647 DOI: 10.1039/d3an00806a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Extracellular vesicles (EVs), which are heterogeneous membrane-based vesicles with bilayer cell membrane structures, could be versatile biomarkers for the identification of diverse diseases including cancers. With this potential, this study has attempted the Raman spectroscopic identification of gall bladder (GB) cancer by directly measuring the EV solution extracted from human bile without further sample drying. For this purpose, bile samples were obtained from four normal individuals and 21 GB polyp, eight hepatocellular carcinoma (HCC), and five GB cancer patients, and EVs were extracted from each of the bile samples. The Raman peak shapes of the EVs extracted from the GB cancer samples, especially the relative intensities of peaks in the 1560-1340 cm-1 range, were dissimilar to those of the samples from the normal, GB polyp, and HCC groups. The intensity ratios of peaks at 1537 and 1453 cm-1 and at 1395 and 1359 cm-1 of the GB cancer samples were lower and higher, respectively, than those of the samples of the remaining three groups. The differences of peak intensity ratios were statistically significant based on the Mann-Whitney U test. DNA/RNA bases, amino acids, and bile salts contributed to the spectra of EVs, and their relative abundances seemed to vary according to the occurrence of GB cancer. The varied metabolite compositions and/or structures of EVs were successfully demonstrated by the dissimilar peak intensity ratios in the Raman spectra, thereby enabling the discrimination of GB cancer.
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Affiliation(s)
- Thu Thuy Bui
- Department of Chemistry and Research Institute for Convergence of Basic Science, Hanyang University, Seoul 04763, Republic of Korea.
| | - Eunjin Jang
- Department of Chemistry and Research Institute for Convergence of Basic Science, Hanyang University, Seoul 04763, Republic of Korea.
| | - Ji Hyun Shin
- Department of Surgery, College of Medicine, Hanyang University, Seoul 04763, Republic of Korea
| | - Tae Hun Kim
- Department of Surgery, College of Medicine, Hanyang University, Seoul 04763, Republic of Korea
| | - Hayoon Kim
- Department of Surgery, College of Medicine, Hanyang University, Seoul 04763, Republic of Korea
| | - Dongho Choi
- Department of Surgery, College of Medicine, Hanyang University, Seoul 04763, Republic of Korea
| | - Tung Duy Vu
- Faculty of Chemistry, University of Science, Vietnam National University, Hanoi, Vietnam
| | - Hoeil Chung
- Department of Chemistry and Research Institute for Convergence of Basic Science, Hanyang University, Seoul 04763, Republic of Korea.
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Ullah A, Huang Y, Zhao K, Hua Y, Ullah S, Rahman MU, Wang J, Wang Q, Hu X, Zheng L. Characteristics and potential clinical applications of the extracellular vesicles of human pathogenic Fungi. BMC Microbiol 2023; 23:227. [PMID: 37598156 PMCID: PMC10439556 DOI: 10.1186/s12866-023-02945-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 07/14/2023] [Indexed: 08/21/2023] Open
Abstract
Extracellular vesicles (EVs) are a heterogeneous group of lipid membrane-enclosed compartments that contain different biomolecules and are released by almost all living cells, including fungal genera. Fungal EVs contain multiple bioactive components that perform various biological functions, such as stimulation of the host immune system, transport of virulence factors, induction of biofilm formation, and mediation of host-pathogen interactions. In this review, we summarize the current knowledge on EVs of human pathogenic fungi, mainly focusing on their biogenesis, composition, and biological effects. We also discuss the potential markers and therapeutic applications of fungal EVs.
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Affiliation(s)
- Amir Ullah
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Yiyi Huang
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Kening Zhao
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
- La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
| | - Yuneng Hua
- Center for Clinical Laboratory, Zhujiang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Shafi Ullah
- Department of pharmacy, COMSATS University Islamabad, Abbottabad Campus, Abbottabad, Pakistan
| | - Mujeeb Ur Rahman
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
| | - Jingyu Wang
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Qian Wang
- Center for Clinical Laboratory, Zhujiang Hospital, Southern Medical University, Guangzhou, People's Republic of China.
| | - Xiumei Hu
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China.
| | - Lei Zheng
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China.
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Won S, Lee C, Bae S, Lee J, Choi D, Kim M, Song S, Lee J, Kim E, Shin H, Basukala A, Lee TR, Lee D, Gho YS. Mass-produced gram-negative bacterial outer membrane vesicles activate cancer antigen-specific stem-like CD8 + T cells which enables an effective combination immunotherapy with anti-PD-1. J Extracell Vesicles 2023; 12:e12357. [PMID: 37563797 PMCID: PMC10415594 DOI: 10.1002/jev2.12357] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 07/24/2023] [Indexed: 08/12/2023] Open
Abstract
Despite the capability of extracellular vesicles (EVs) derived from Gram-negative and Gram-positive bacteria to induce potent anti-tumour responses, large-scale production of bacterial EVs remains as a hurdle for their development as novel cancer immunotherapeutic agents. Here, we developed manufacturing processes for mass production of Escherichia coli EVs, namely, outer membrane vesicles (OMVs). By combining metal precipitation and size-exclusion chromatography, we isolated 357 mg in total protein amount of E. coli OMVs, which was equivalent to 3.93 × 1015 particles (1.10 × 1010 particles/μg in total protein amounts of OMVs) from 160 L of the conditioned medium. We show that these mass-produced E. coli OMVs led to complete remission of two mouse syngeneic tumour models. Further analysis of tumour microenvironment in neoantigen-expressing tumour models revealed that E. coli OMV treatment causes increased infiltration and activation of CD8+ T cells, especially those of cancer antigen-specific CD8+ T cells with high expression of TCF-1 and PD-1. Furthermore, E. coli OMVs showed synergistic anti-tumour activity with anti-PD-1 antibody immunotherapy, inducing substantial tumour growth inhibition and infiltration of activated cancer antigen-specific stem-like CD8+ T cells into the tumour microenvironment. These data highlight the potent anti-tumour activities of mass-produced E. coli OMVs as a novel candidate for developing next-generation cancer immunotherapeutic agents.
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Affiliation(s)
- Solchan Won
- Department of Biomedical SciencesSeoul National University College of MedicineSeoulRepublic of Korea
| | | | - Seoyoon Bae
- Department of Life SciencesPOSTECHPohangRepublic of Korea
| | - Jaemin Lee
- SL Bigen Inc.IncheonRepublic of Korea
- Department of Life SciencesPOSTECHPohangRepublic of Korea
| | - Dongsic Choi
- Department of BiochemistrySoonchunhyang University College of MedicineCheonanRepublic of Korea
| | - Min‐Gang Kim
- Department of Biomedical SciencesSeoul National University College of MedicineSeoulRepublic of Korea
| | | | | | - Eunhye Kim
- Department of Biomedical SciencesSeoul National University College of MedicineSeoulRepublic of Korea
| | - HaYoung Shin
- Department of Life SciencesPOSTECHPohangRepublic of Korea
| | - Anita Basukala
- Department of Life SciencesPOSTECHPohangRepublic of Korea
| | | | - Dong‐Sup Lee
- Department of Biomedical SciencesSeoul National University College of MedicineSeoulRepublic of Korea
| | - Yong Song Gho
- SL Bigen Inc.IncheonRepublic of Korea
- Department of Life SciencesPOSTECHPohangRepublic of Korea
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Sun J, Li Q, Ding Y, Wei D, Hadisurya M, Luo Z, Gu Z, Chen B, Tao WA. Profiling Phosphoproteome Landscape in Circulating Extracellular Vesicles from Microliters of Biofluids through Functionally Tunable Paramagnetic Separation. Angew Chem Int Ed Engl 2023; 62:e202305668. [PMID: 37216424 PMCID: PMC11019431 DOI: 10.1002/anie.202305668] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/17/2023] [Accepted: 05/22/2023] [Indexed: 05/24/2023]
Abstract
Many biological processes are regulated through dynamic protein phosphorylation. Monitoring disease-relevant phosphorylation events in circulating biofluids is highly appealing but also technically challenging. We introduce here a functionally tunable material and a strategy, extracellular vesicles to phosphoproteins (EVTOP), which achieves one-pot extracellular vesicles (EVs) isolation, extraction, and digestion of EV proteins, and enrichment of phosphopeptides, with only a trace amount of starting biofluids. EVs are efficiently isolated by magnetic beads functionalized with TiIV ions and a membrane-penetrating peptide, octa-arginine R8 + , which also provides the hydrophilic surface to retain EV proteins during lysis. Subsequent on-bead digestion concurrently converts EVTOP to TiIV ion-only surface for efficient enrichment of phosphopeptides for phosphoproteomic analyses. The streamlined, ultra-sensitive platform enabled us to quantify 500 unique EV phosphopeptides with only a few μL of plasma and over 1200 phosphopeptides with 100 μL of cerebrospinal fluid (CSF). We explored its clinical application of monitoring the outcome of chemotherapy of primary central nervous system lymphoma (PCNSL) patients with a small volume of CSF, presenting a powerful tool for broad clinical applications.
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Affiliation(s)
- Jie Sun
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, Southeast University, Nanjing, China
| | - Qing Li
- Department of Hematology, Huashan Hospital, Shanghai, China
| | - Yajie Ding
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, Southeast University, Nanjing, China
| | - Dong Wei
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, Southeast University, Nanjing, China
| | - Marco Hadisurya
- Department of Biochemistry, Department of Biochemistry, Purdue University, West Lafayette, IN 47907; Institute for Cancer ResearchPurdue University West Lafayette, IN47907
| | - Zhuojun Luo
- Department of Biochemistry, Department of Biochemistry, Purdue University, West Lafayette, IN 47907; Institute for Cancer ResearchPurdue University West Lafayette, IN47907
| | - Zhongze Gu
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, Southeast University, Nanjing, China
| | - Bobin Chen
- Department of Hematology, Huashan Hospital, Shanghai, China
| | - W. Andy Tao
- Department of Biochemistry, Department of Biochemistry, Purdue University, West Lafayette, IN 47907; Institute for Cancer ResearchPurdue University West Lafayette, IN47907
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Trappe A, Lakkappa N, Carter S, Dillon E, Wynne K, McKone E, McNally P, Coppinger JA. Investigating serum extracellular vesicles in Cystic Fibrosis. J Cyst Fibros 2023; 22:674-679. [PMID: 36858853 DOI: 10.1016/j.jcf.2023.02.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 02/02/2023] [Accepted: 02/10/2023] [Indexed: 03/02/2023]
Abstract
BACKGROUND Extracellular vesicles (EVs) are emerging as biomarkers of disease with diagnostic potential in CF. With the advent of highly effective modulator therapy, sputum production is less common and there is a need to identify novel markers of CF disease progression, exacerbation and response to therapies in accessible fluids such as serum. METHODS We used size exclusion chromatography (SEC) to isolate and characterise EVs from the blood of PWCF of different ages and compared to ultracentrifugation (UC). We used nanoparticle tracking analysis to measure the number of EVs present in serum obtained from children and adults with CF. Mass spectrometry based proteomics was used to characterise protein expression changes between the groups. RESULTS EVs were successfully isolated in SEC fractions from 250 µl serum from PWCF in greater numbers (p <0.01) than density ultracentrifugation. There was not a significant difference in EV numbers between young children with CF and controls. However, there was significantly more EVs in adults compared to children (<6yrs) (p < 0.05). EVs from PWCF before and after Kaftrio treatment were also analysed. Significant protein expression changes were observed within all 3 group. The largest changes detected were between children and adults with CF (57 proteins had a 1.5 fold change in expression with 19 significant changes p < 0.05) and PWCF taking Kaftrio (24 significant changes in EV protein expression was observed 12 months post treatment). CONCLUSION In this pilot study, we performed an initial characterisation of EVs in serum from PWCF demonstrating the potential of serum EVs for further diagnostic investigation.
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Affiliation(s)
- Anne Trappe
- National Children's Research Centre, Children's Health Ireland, Dublin 12, Ireland; School of Pharmacy and Biomolecular Sciences, RCSI University of Medicine and Health Sciences, Dublin 2, Ireland
| | - Navya Lakkappa
- National Children's Research Centre, Children's Health Ireland, Dublin 12, Ireland; School of Pharmacy and Biomolecular Sciences, RCSI University of Medicine and Health Sciences, Dublin 2, Ireland
| | | | - Eugene Dillon
- Systems Biology Ireland, University College Dublin, Dublin 4, Ireland
| | - Kieran Wynne
- Systems Biology Ireland, University College Dublin, Dublin 4, Ireland
| | - Edward McKone
- St. Vincent's University Hospital, Dublin 4, Ireland
| | - Paul McNally
- National Children's Research Centre, Children's Health Ireland, Dublin 12, Ireland; Department of Paediatrics, RCSI University of Medicine and Health Sciences, Dublin 2, Ireland
| | - Judith A Coppinger
- National Children's Research Centre, Children's Health Ireland, Dublin 12, Ireland; School of Pharmacy and Biomolecular Sciences, RCSI University of Medicine and Health Sciences, Dublin 2, Ireland.
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Cumba Garcia LM, Bouchal SM, Bauman MMJ, Parney IF. Advancements and Technical Considerations for Extracellular Vesicle Isolation and Biomarker Identification in Glioblastoma. Neurosurgery 2023; 93:33-42. [PMID: 36749103 DOI: 10.1227/neu.0000000000002393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 12/06/2022] [Indexed: 02/08/2023] Open
Abstract
Extracellular vesicles (EVs) are membrane-bound particles released by all cells. Previous research has found that these microscopic vesicles contribute to intercellular signaling and communication. EVs carry a variety of cargo, including nucleic acids, proteins, metabolites, and lipids. The composition of EVs varies based on cell of origin. Therefore, EVs can serve as an important biomarker in the diagnosis and treatment of various cancers. EVs derived from glioblastoma (GBM) cells carry biomarkers, which could serve as the basis for a potential diagnostic strategy known as liquid biopsy. Multiple EV isolation techniques exist, including ultrafiltration, size exclusion chromatography, flow field-flow fractionation, sequential filtration, differential ultracentrifugation, and density-gradient ultracentrifugation. Recent and ongoing work aims to identify cellular markers to distinguish GBM-derived EVs from those released by noncancerous cells. Strategies include proteomic analysis of GBM EVs, identification of GBM-specific metabolites, and use of Food and Drug Administration-approved 5-aminolevulinic acid-an oral agent that causes fluorescence of GBM cells-to recognize GBM EVs in a patient's blood. In addition, accurately and precisely monitoring changes in EV cargo concentrations could help differentiate between pseudoprogression and GBM recurrence, thus preventing unnecessary surgical interventions.
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Affiliation(s)
- Luz M Cumba Garcia
- Department of Immunology, Mayo Clinic Graduate School of Biomedical Sciences, Rochester, Minnesota, USA
| | - Samantha M Bouchal
- Mayo Clinic Alix School of Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Megan M J Bauman
- Mayo Clinic Alix School of Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Ian F Parney
- Department of Neurological Surgery, Mayo Clinic, Rochester, Minnesota, USA
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Mishra S, Kumar A, Kim S, Su Y, Singh S, Sharma M, Almousa S, Rather HA, Jain H, Lee J, Furdui CM, Ahmad S, Ferrario CM, Punzi HA, Chuang CC, Wabitsch M, Kritchevsky SB, Register TC, Deep G. A Liquid Biopsy-Based Approach to Isolate and Characterize Adipose Tissue-Derived Extracellular Vesicles from Blood. ACS Nano 2023; 17:10252-10268. [PMID: 37224410 DOI: 10.1021/acsnano.3c00422] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Obesity is a major risk factor for multiple chronic diseases. Anthropometric and imaging approaches are primarily used to assess adiposity, and there is a dearth of techniques to determine the changes in adipose tissue (AT) at the molecular level. Extracellular vesicles (EVs) have emerged as a novel and less invasive source of biomarkers for various pathologies. Furthermore, the possibility of enriching cell or tissue-specific EVs from the biofluids based on their unique surface markers has led to classifying these vesicles as "liquid biopsies", offering valuable molecular information on hard-to-access tissues. Here, we isolated small EVs from AT (sEVAT) of lean and diet-induced obese (DIO) mice, identified unique surface proteins on sEVAT by surface shaving followed by mass spectrometry, and developed a signature of five unique proteins. Using this signature, we pulled out sEVAT from the blood of mice and validated the specificity of isolated sEVAT by measuring the expression of adiponectin, 38 adipokines on an array, and several adipose tissue-related miRNAs. Furthermore, we provided evidence of sEV applicability in disease prediction by characterizing sEVAT from the blood of lean and DIO mice. Interestingly, sEVAT-DIO cargo showed a stronger pro-inflammatory effect on THP1 monocytes compared to sEVAT-Lean and a significant increase in obesity-associated miRNA expression. Equally important, sEVAT cargo revealed an obesity-associated aberrant amino acid metabolism that was subsequently validated in the corresponding AT. Lastly, we show a significant increase in inflammation-related molecules in sEVAT isolated from the blood of nondiabetic obese (>30 kg/m2) individuals. Overall, the present study offers a less-invasive approach to characterize AT.
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Affiliation(s)
- Shalini Mishra
- Department of Cancer Biology, Wake Forest University School of Medicine, Winston-Salem, North Carolina 27157, United States
| | - Ashish Kumar
- Department of Cancer Biology, Wake Forest University School of Medicine, Winston-Salem, North Carolina 27157, United States
| | - Susy Kim
- Department of Cancer Biology, Wake Forest University School of Medicine, Winston-Salem, North Carolina 27157, United States
| | - Yixin Su
- Department of Cancer Biology, Wake Forest University School of Medicine, Winston-Salem, North Carolina 27157, United States
| | - Sangeeta Singh
- Department of Cancer Biology, Wake Forest University School of Medicine, Winston-Salem, North Carolina 27157, United States
| | - Mitu Sharma
- Department of Cancer Biology, Wake Forest University School of Medicine, Winston-Salem, North Carolina 27157, United States
| | - Sameh Almousa
- Department of Cancer Biology, Wake Forest University School of Medicine, Winston-Salem, North Carolina 27157, United States
| | - Hilal A Rather
- Department of Cancer Biology, Wake Forest University School of Medicine, Winston-Salem, North Carolina 27157, United States
| | - Heetanshi Jain
- Department of Cancer Biology, Wake Forest University School of Medicine, Winston-Salem, North Carolina 27157, United States
| | - Jingyun Lee
- Wake Forest Baptist Comprehensive Cancer Center, Winston-Salem, North Carolina 27157, United States
| | - Cristina M Furdui
- Wake Forest Baptist Comprehensive Cancer Center, Winston-Salem, North Carolina 27157, United States
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest University School of Medicine, Winston-Salem, North Carolina 27157, United States
| | - Sarfaraz Ahmad
- Laboratory of Translational Hypertension, Department of General Surgery, Wake Forest University School of Medicine, Winston-Salem, North Carolina 27157, United States
| | - Carlos M Ferrario
- Laboratory of Translational Hypertension, Department of General Surgery, Wake Forest University School of Medicine, Winston-Salem, North Carolina 27157, United States
| | - Henry A Punzi
- Punzi Medical Center, Punzi Institute of Medicine, Carrollton, Texas 75006, United States
- UT Southwestern Medical Center, Dallas, Texas, 75390, United States
| | - Chia-Chi Chuang
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest University School of Medicine, Winston-Salem, North Carolina 27157, United States
| | - Martin Wabitsch
- Department of Pediatrics and Adolescent Medicine, Center for Rare Endocrine Diseases, Ulm University Medical Centre, Ulm 89069, Germany
| | - Stephen B Kritchevsky
- Department of Internal Medicine-Gerontology and Geriatric Medicine, Wake Forest University School of Medicine, Winston-Salem, North Carolina 27157, United States
- Sticht Center for Healthy Aging and Alzheimer's Prevention, Wake Forest University School of Medicine, Winston-Salem, North Carolina 27157, United States
| | - Thomas C Register
- Sticht Center for Healthy Aging and Alzheimer's Prevention, Wake Forest University School of Medicine, Winston-Salem, North Carolina 27157, United States
- Department of Pathology, Section on Comparative Medicine, Wake Forest University School of Medicine, Winston-Salem, North Carolina 27157, United States
| | - Gagan Deep
- Department of Cancer Biology, Wake Forest University School of Medicine, Winston-Salem, North Carolina 27157, United States
- Wake Forest Baptist Comprehensive Cancer Center, Winston-Salem, North Carolina 27157, United States
- Sticht Center for Healthy Aging and Alzheimer's Prevention, Wake Forest University School of Medicine, Winston-Salem, North Carolina 27157, United States
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Zhou Y, Yuan R, Cone AS, Shifflett KW, Arias GF, Peng A, Chambers MG, McNamara RP, Willcox S, Landis JT, Pan Y, Griffith J, Dittmer DP. Large-scale heparin-based bind-and-elute chromatography identifies two biologically distinct populations of extracellular vesicles. J Extracell Vesicles 2023; 12:e12327. [PMID: 37272197 PMCID: PMC10240191 DOI: 10.1002/jev2.12327] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 04/10/2023] [Accepted: 04/20/2023] [Indexed: 06/06/2023] Open
Abstract
Purifying extracellular vesicles (EVs) has been challenging because EVs are heterogeneous in cargo yet share similar sizes and densities. Most surface marker-based affinity separation methods are limited to research or diagnostic scales. We report that heparin chromatography can separate purified EVs into two distinct subpopulations as ascertained by MS/MS: a non-heparin-binding (NHB) fraction that contains classical EV markers such as tetraspanins and a heparin-binding (HB) fraction enriched in fibronectins and histones. Both fractions were similarly fusogenic but induced different transcriptional responses in endothelial cells. While EVs that were purified by conventional, non-affinity methods alone induced ERK1/2 phosphorylation and Ki67, the NHB fraction did not. This result suggests heparin chromatography as an additional novel fractionation step that is inherently scalable, does not lead to loss of material, and separates inflammatory and pyrogenic EVs from unreactive EVs, which will improve clinical applications.
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Affiliation(s)
- Yijun Zhou
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Runjie Yuan
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Allaura S Cone
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Kyle W Shifflett
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Gabriel F Arias
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Alice Peng
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Meredith G Chambers
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Ryan P McNamara
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Smaranda Willcox
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Justin T Landis
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Yue Pan
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Biostatistics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jack Griffith
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Dirk P Dittmer
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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Keysberg C, Schneider H, Otte K. Production cell analysis and compound-based boosting of small extracellular vesicle secretion using a generic and scalable production platform. Biotechnol Bioeng 2023; 120:987-999. [PMID: 36577715 DOI: 10.1002/bit.28322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 12/07/2022] [Accepted: 12/28/2022] [Indexed: 12/30/2022]
Abstract
Extracellular vesicles (EVs) are a novel format of advanced therapeutical medicinal products (ATMPs). They can act regenerative or immune-modulatory as cell therapy substitutes or as a platform for designer exosomes. The biotechnological production of therapeutic EVs is still very much uncharted territory so standardized host cells, production setups, and isolation methods are not yet implemented. In this work, we present a tangential flow filtration (TFF) and fast-performance liquid chromatography (FPLC)-based size exclusion chromatography (SEC) purification setup that is compatible for industry applications. Moreover, we evaluated a series of potential host cell lines regarding their EV productivity, characteristics, and biological functionality. It was found that telomerase-immortalized Wharton's jelly mesenchymal stromal cells (WJ-MSC/TERT273) secrete high amounts of EVs per cell with regenerative capabilities. On the other hand, Cevec's amniocyte producer cells® (CAP®) and human embryonic kidney (HEK293) suspension cells are suitable platforms for designer EVs with high yields. Finally, we aimed to boost the EV secretion of HEK293 cells via chemical adjuvants and verified four compounds that heighten cellular EV secretion in a presumably cAMP-dependent manner. A combination of fenoterol, iodoacetamide, and dinitrophenol increased the EV yield in HEK293 cells threefold and cellular secretion rate fivefold.
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Affiliation(s)
- Christoph Keysberg
- Institute for Applied Biotechnology, University of Applied Sciences Biberach, Biberach, Germany
- International Graduate School for Molecular Medicine, Ulm University, Ulm, Germany
| | - Helga Schneider
- Institute for Applied Biotechnology, University of Applied Sciences Biberach, Biberach, Germany
| | - Kerstin Otte
- Institute for Applied Biotechnology, University of Applied Sciences Biberach, Biberach, Germany
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50
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Raizada G, Namasivayam B, Obeid S, Brunel B, Boireau W, Lesniewska E, Elie-Caille C. Multimodal Analytical Platform on a Multiplexed Surface Plasmon Resonance Imaging Chip for the Analysis of Extracellular Vesicle Subsets. J Vis Exp 2023. [PMID: 37010274 DOI: 10.3791/64210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2023] Open
Abstract
Extracellular vesicles (EVs) are membrane-derived, tiny vesicles produced by all cells that range from 50 to several hundreds of nanometers in diameter and are used as a means of intercellular communication. They are emerging as promising diagnostic and therapeutic tools for a variety of diseases. There are two main biogenesis processes used by cells to produce EVs with differences in size, composition, and content. Due to their high complexity in size, composition, and cell origin, their characterization requires a combination of analytical techniques. This project involves the development of a new generation of multiparametric analytical platforms with increased throughput for the characterization of subpopulations of EVs. To achieve this goal, the work starts from the nanobioanalytical platform (NBA) established by the group, which allows an original investigation of EVs based on a combination of multiplexed biosensing methods with metrological and morphomechanical analyses by atomic force microscopy (AFM) of vesicular targets trapped on a microarray biochip. The objective was to complete this EV investigation with a phenotypic and molecular analysis by Raman spectroscopy. These developments enable the proposal of a multimodal and easy-to-use analytical solution for the discrimination of EV subsets in biological fluids with clinical potential.
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Affiliation(s)
- Geetika Raizada
- Université de Franche-Comté, CNRS UMR-6174, FEMTO-ST Institute
| | | | - Sameh Obeid
- Institut Galien Paris-Saclay, CNRS UMR-8612 , Université Paris-Saclay
| | - Benjamin Brunel
- Université de Franche-Comté, CNRS UMR-6174, FEMTO-ST Institute
| | - Wilfrid Boireau
- Université de Franche-Comté, CNRS UMR-6174, FEMTO-ST Institute
| | - Eric Lesniewska
- Interdisciplinary Lab Carnot Bourgogne LICB, CNRS UMR-6303, Université de Bourgogne Franche-Comté
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