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Aresta AM, De Vietro N, Zambonin C. Analysis and Characterization of the Extracellular Vesicles Released in Non-Cancer Diseases Using Matrix-Assisted Laser Desorption Ionization/Mass Spectrometry. Int J Mol Sci 2024; 25:4490. [PMID: 38674075 PMCID: PMC11050240 DOI: 10.3390/ijms25084490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 04/09/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
The extracellular vesicles (EVs) released by cells play a crucial role in intercellular communications and interactions. The direct shedding of EVs from the plasma membrane represents a fundamental pathway for the transfer of properties and information between cells. These vesicles are classified based on their origin, biogenesis, size, content, surface markers, and functional features, encompassing a variety of bioactive molecules that reflect the physiological state and cell type of origin. Such molecules include lipids, nucleic acids, and proteins. Research efforts aimed at comprehending EVs, including the development of strategies for their isolation, purification, and characterization, have led to the discovery of new biomarkers. These biomarkers are proving invaluable for diagnosing diseases, monitoring disease progression, understanding treatment responses, especially in oncology, and addressing metabolic, neurological, infectious disorders, as well as advancing vaccine development. Matrix-Assisted Laser Desorption Ionization (MALDI)/Mass Spectrometry (MS) stands out as a leading tool for the analysis and characterization of EVs and their cargo. This technique offers inherent advantages such as a high throughput, minimal sample consumption, rapid and cost-effective analysis, and user-friendly operation. This review is mainly focused on the primary applications of MALDI-time-of-flight (TOF)/MS in the analysis and characterization of extracellular vesicles associated with non-cancerous diseases and pathogens that infect humans, animals, and plants.
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Affiliation(s)
- Antonella Maria Aresta
- Department of Biosciences, Biotechnology and Environment, University of Bari “Aldo Moro”, Via E. Orabona 4, 70126 Bari, Italy; (N.D.V.)
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Pang JL, Shao H, Xu XG, Lin ZW, Chen XY, Chen JY, Mou XZ, Hu PY. Targeted drug delivery of engineered mesenchymal stem/stromal-cell-derived exosomes in cardiovascular disease: recent trends and future perspectives. Front Bioeng Biotechnol 2024; 12:1363742. [PMID: 38558788 PMCID: PMC10978787 DOI: 10.3389/fbioe.2024.1363742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Accepted: 02/20/2024] [Indexed: 04/04/2024] Open
Abstract
In recent years, stem cells and their secretomes, notably exosomes, have received considerable attention in biomedical applications. Exosomes are cellular secretomes used for intercellular communication. They perform the function of intercellular messengers by facilitating the transport of proteins, lipids, nucleic acids, and therapeutic substances. Their biocompatibility, minimal immunogenicity, targetability, stability, and engineerable characteristics have additionally led to their application as drug delivery vehicles. The therapeutic efficacy of exosomes can be improved through surface modification employing functional molecules, including aptamers, antibodies, and peptides. Given their potential as targeted delivery vehicles to enhance the efficiency of treatment while minimizing adverse effects, exosomes exhibit considerable promise. Stem cells are considered advantageous sources of exosomes due to their distinctive characteristics, including regenerative and self-renewal capabilities, which make them well-suited for transplantation into injured tissues, hence promoting tissue regeneration. However, there are notable obstacles that need to be addressed, including immune rejection and ethical problems. Exosomes produced from stem cells have been thoroughly studied as a cell-free strategy that avoids many of the difficulties involved with cell-based therapy for tissue regeneration and cancer treatment. This review provides an in-depth summary and analysis of the existing knowledge regarding exosomes, including their engineering and cardiovascular disease (CVD) treatment applications.
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Affiliation(s)
- Jian-Liang Pang
- Department of Vascular Surgery, Tiantai People’s Hospital of Zhejiang Province (Tiantai Branch of Zhejiang People’s Hospital), Taizhou, Zhejiang, China
| | - Hong Shao
- Department of Vascular Surgery, Tiantai People’s Hospital of Zhejiang Province (Tiantai Branch of Zhejiang People’s Hospital), Taizhou, Zhejiang, China
- Department of Cardiovascular Medicine, Heart Center, Zhejiang Provincial People’s Hospital (Affiliated People’s Hospital), Hangzhou Medical College, Hangzhou, China
| | - Xiao-Gang Xu
- Clinical Research Institute, Zhejiang Provincial People’s Hospital (Affiliated People’s Hospital), Hangzhou Medical College, Hangzhou, China
| | - Zhi-Wei Lin
- Zhejiang Healthfuture Biomedicine Co., Ltd., Hangzhou, China
| | - Xiao-Yi Chen
- Clinical Research Institute, Zhejiang Provincial People’s Hospital (Affiliated People’s Hospital), Hangzhou Medical College, Hangzhou, China
| | - Jin-Yang Chen
- Zhejiang Healthfuture Biomedicine Co., Ltd., Hangzhou, China
| | - Xiao-Zhou Mou
- Clinical Research Institute, Zhejiang Provincial People’s Hospital (Affiliated People’s Hospital), Hangzhou Medical College, Hangzhou, China
| | - Pei-Yang Hu
- Department of Traumatology, Tiantai People’s Hospital of Zhejiang Province (Tiantai Branch of Zhejiang People’s Hospital), Taizhou, China
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Zhao Z, Yang S, Tang X, Feng L, Ding Z, Chen Z, Luo X, Deng R, Sheng J, Xie S, Chang K, Chen M. DNA four-way junction-driven dual-rolling circle amplification sandwich-type aptasensor for ultra-sensitive and specific detection of tumor-derived exosomes. Biosens Bioelectron 2024; 246:115841. [PMID: 38006701 DOI: 10.1016/j.bios.2023.115841] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 11/10/2023] [Accepted: 11/12/2023] [Indexed: 11/27/2023]
Abstract
There is an urgent need to accurately quantify tumor-derived exosomes, which have emerged as promising non-invasive tumor diagnostic biomarkers. Herein, a bispecific-aptamer sandwich-type gold nanoparticle-modified electrochemical aptasensor was developed based on a four-way junction (4-WJ)-triggered dual rolling circle amplification (RCA)-assisted methylene blue (MB)/G-quadruplex strategy for extremely specific and sensitive exosome detection. This aptamer/exosome/aptamer sandwich-type design contained a CD63-specific aptamer and a cancerous mucin-1 (MUC1) protein-specific aptamer. The CD63 aptamer modified on a gold electrode captured exosomes, and then the sandwich-type aptasensor was formed with the addition of the MUC1 aptamer. The MUC1 aptamer's 3'-end sequence facilitated the formation of 4-WJ, assisted by a molecular beacon probe and a binary DNA probe. Subsequently, a dual-RCA reaction was triggered by binding to two cytosine-rich circle DNA templates at both ends of 4-WJ. Ultimately, dual-RCA products containing multiple G-quadruplex conformations were generated with the assistance of K+ to trap abundant MB indicators and amplify electrochemical signals. The aptasensor exhibited high specificity, sensitivity, repeatability, and stability toward MCF-7-derived exosomes, with a detection limit of 20 particles/mL and a linear range of 1 × 102 to 1 × 107 particles/mL. Moreover, it showed excellent applicability in clinical settings to recover exosomes in normal human serum. Our aptasensor is anticipated to serve as a versatile platform for detecting various specific aptamer-based targets in biomedical and bioanalytical applications.
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Affiliation(s)
- Zhuyang Zhao
- Department of Clinical Laboratory Medicine, Southwest Hospital, Army Medical University (Third Military Medical University), 30 Gaotanyan, Shapingba District, Chongqing, 400038, China
| | - Sha Yang
- Department of Clinical Laboratory Medicine, Southwest Hospital, Army Medical University (Third Military Medical University), 30 Gaotanyan, Shapingba District, Chongqing, 400038, China
| | - Xiaoqi Tang
- Department of Clinical Laboratory Medicine, Southwest Hospital, Army Medical University (Third Military Medical University), 30 Gaotanyan, Shapingba District, Chongqing, 400038, China
| | - Liu Feng
- Department of Clinical Laboratory Medicine, Southwest Hospital, Army Medical University (Third Military Medical University), 30 Gaotanyan, Shapingba District, Chongqing, 400038, China
| | - Zishan Ding
- Department of Clinical Laboratory Medicine, Southwest Hospital, Army Medical University (Third Military Medical University), 30 Gaotanyan, Shapingba District, Chongqing, 400038, China
| | - Zhiguo Chen
- Department of Clinical Laboratory Medicine, Southwest Hospital, Army Medical University (Third Military Medical University), 30 Gaotanyan, Shapingba District, Chongqing, 400038, China
| | - Xing Luo
- Department of Clinical Laboratory Medicine, Southwest Hospital, Army Medical University (Third Military Medical University), 30 Gaotanyan, Shapingba District, Chongqing, 400038, China
| | - Ruijia Deng
- Department of Clinical Laboratory Medicine, Southwest Hospital, Army Medical University (Third Military Medical University), 30 Gaotanyan, Shapingba District, Chongqing, 400038, China
| | - Jing Sheng
- Department of Clinical Laboratory Medicine, Southwest Hospital, Army Medical University (Third Military Medical University), 30 Gaotanyan, Shapingba District, Chongqing, 400038, China
| | - Shuang Xie
- Department of Clinical Laboratory Medicine, Southwest Hospital, Army Medical University (Third Military Medical University), 30 Gaotanyan, Shapingba District, Chongqing, 400038, China
| | - Kai Chang
- Department of Clinical Laboratory Medicine, Southwest Hospital, Army Medical University (Third Military Medical University), 30 Gaotanyan, Shapingba District, Chongqing, 400038, China.
| | - Ming Chen
- Department of Clinical Laboratory Medicine, Southwest Hospital, Army Medical University (Third Military Medical University), 30 Gaotanyan, Shapingba District, Chongqing, 400038, China; College of Pharmacy and Laboratory Medicine, Army Medical University (Third Military Medical University), 30 Gaotanyan, Shapingba District, Chongqing, 400038, China.
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4
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Abhange K, Kitata RB, Zhang J, Wang YT, Gaffrey MJ, Liu T, Gunchick V, Khaykin V, Sahai V, Cuneo KC, Parikh ND, Shi T, Lubman DM. In-Depth Proteome Profiling of Small Extracellular Vesicles Isolated from Cancer Cell Lines and Patient Serum. J Proteome Res 2024; 23:386-396. [PMID: 38113368 PMCID: PMC10947532 DOI: 10.1021/acs.jproteome.3c00614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Extracellular vesicle (EV) secretion has been observed in many types of both normal and tumor cells. EVs contain a variety of distinctive cargoes, allowing tumor-derived serum proteins in EVs to act as a minimally invasive method for clinical monitoring. We have undertaken a comprehensive study of the protein content of the EVs from several cancer cell lines using direct data-independent analysis. Several thousand proteins were detected, including many classic EV markers such as CD9, CD81, CD63, TSG101, and Syndecan-1, among others. We detected many distinctive cancer-specific proteins, including several known markers used in cancer detection and monitoring. We further studied the protein content of EVs from patient serum for both normal controls and pancreatic cancer and hepatocellular carcinoma. The EVs for these studies have been isolated by various methods for comparison, including ultracentrifugation and CD9 immunoaffinity column. Typically, 500-1000 proteins were identified, where most of them overlapped with the EV proteins identified from the cell lines studied. We were able to identify many of the cell-line EV protein markers in the serum EVs, in addition to the large numbers of proteins specific to pancreatic and HCC cancers.
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Affiliation(s)
- Komal Abhange
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, Michigan 48109, United States
| | - Reta Birhanu Kitata
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Jie Zhang
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, Michigan 48109, United States
| | - Yi-Ting Wang
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Matthew J Gaffrey
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Valerie Gunchick
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Valerie Khaykin
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Vaibhav Sahai
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Kyle C Cuneo
- Department of Radiation Oncology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Neehar D Parikh
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Tujin Shi
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - David M Lubman
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, Michigan 48109, United States
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Wang Z, Zhang Z, Zhang Y, Xu X, Shen T, Pan H, Chang D. MXenes-Au NPs modified electrochemical biosensor for multiple exosome surface proteins analysis. Talanta 2023; 265:124848. [PMID: 37352782 DOI: 10.1016/j.talanta.2023.124848] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 05/22/2023] [Accepted: 06/19/2023] [Indexed: 06/25/2023]
Abstract
As a novel class of non-invasive biomarkers, exosome-carried proteins are essential in early detection and precise cancer diagnosis. In the study, we developed an electrochemical biosensor based on MXenes-Au NPs modification to assess the differential expression of EGFR, CEA, and EpCAM proteins of exosomes. This sensor has sensitively detected tumor biomarkers in the exosomes generated by various tumor cells (including A549, MCF-7, PC-3, and HeLa). Building a biosensor that can distinguish minute differences of proteins in various derived-from exosomes is crucial for addressing the issues with early and accurate cancer detection.
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Affiliation(s)
- Zhangmin Wang
- Department of Clinical Laboratory, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai, 201399, China
| | - Ze Zhang
- Department of Clinical Laboratory, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai, 201399, China
| | - Yingcong Zhang
- Department of Clinical Laboratory, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Xin Xu
- Department of Clinical Laboratory, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai, 201399, China
| | - Tong Shen
- Department of Clinical Laboratory, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai, 201399, China
| | - Hongzhi Pan
- Collaborative Research Center, Shanghai University of Medicine and Health Sciences, Shanghai, 201399, China.
| | - Dong Chang
- Department of Clinical Laboratory, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai, 201399, China.
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Altıntaş Ö, Saylan Y. Exploring the Versatility of Exosomes: A Review on Isolation, Characterization, Detection Methods, and Diverse Applications. Anal Chem 2023; 95:16029-16048. [PMID: 37874907 DOI: 10.1021/acs.analchem.3c02224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2023]
Abstract
Extracellular vesicles (EVs) are crucial mediators of intercellular communication and can be classified based on their physical properties, biomolecular structure, and origin. Among EVs, exosomes have garnered significant attention due to their potential as therapeutic and diagnostic tools. Exosomes are released via fusion of multivesicular bodies on plasma membranes and can be isolated from various biofluids using methods such as differential ultracentrifugation, immune affinity capture, ultrafiltration, and size exclusion chromatography. Herein, an overview of different techniques for exosome characterization and isolation, as well as the diverse applications of exosome detection, including their potential use in drug delivery and disease diagnosis, is provided. Additionally, we discuss the emerging field of exosome detection by sensors, which offers an up-and-coming avenue for point-of-care diagnostic tools development. Overall, this review aims to provide a exhaustive and up-to-date summary of the current state of exosome research.
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Affiliation(s)
- Özge Altıntaş
- Hacettepe University, Department of Chemistry, 06800 Ankara, Turkey
| | - Yeşeren Saylan
- Hacettepe University, Department of Chemistry, 06800 Ankara, Turkey
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7
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Park S, Jalaludin I, Hwang H, Ko M, Adelipour M, Hwan M, Cho N, Kim KK, Lubman DM, Kim J. Size-exclusion chromatography for the characterization of urinary extracellular vesicles. J Chromatogr B Analyt Technol Biomed Life Sci 2023; 1228:123828. [PMID: 37480686 PMCID: PMC10530618 DOI: 10.1016/j.jchromb.2023.123828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 07/07/2023] [Accepted: 07/12/2023] [Indexed: 07/24/2023]
Abstract
In recent years, extracellular vesicles (EVs) have gained attention for their potential as biomarkers for the early diagnosis and treatment of various diseases. Traditionally, EV isolation has relied exclusively on ultracentrifugation. However, alternative enrichment methods such as size-exclusion chromatography (SEC) and polyethylene glycol-based precipitation have been introduced. This study utilized SEC as a characterization tool to assess the efficiency of EV isolation. Urinary EVs isolated from human urine using centrifugation (40,000 × g) were analyzed using an SEC column with a pore size of 1000 Å, an inner diameter of 7.8 mm, and a length of 300 mm. The EVs were detected sequentially using UV (280 nm) and fluorescence (λex/em = 550 nm/565 nm); the EVs were observed at approximately 6 min, while the proteins were observed at approximately 12 min. The repeated centrifugation enrichment steps resulted in an increase in EV peaks and a decrease in protein peaks. SEC analysis of the enriched EV samples confirmed that a four-cycle repetition of centrifugation is necessary for successful EV enrichment and removal of non-EV proteins from 40 mL of human urine.
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Affiliation(s)
- Sanghwi Park
- Department of Chemistry, Chungnam National University, Daejeon, Republic of Korea
| | - Iqbal Jalaludin
- Department of Chemistry, Chungnam National University, Daejeon, Republic of Korea; Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru, 81310 Johor, Malaysia
| | - Hyojin Hwang
- Department of Chemistry, Chungnam National University, Daejeon, Republic of Korea
| | - Minjeong Ko
- Department of Chemistry, Chungnam National University, Daejeon, Republic of Korea
| | - Maryam Adelipour
- Department of Chemistry, Chungnam National University, Daejeon, Republic of Korea; Department of Biochemistry, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Myung Hwan
- Department of Chemistry, Chungnam National University, Daejeon, Republic of Korea
| | - Namjoon Cho
- Department of Biochemistry, Chungnam National University, Daejeon, Republic of Korea
| | - Kee K Kim
- Department of Biochemistry, Chungnam National University, Daejeon, Republic of Korea
| | - David M Lubman
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, MI, USA
| | - Jeongkwon Kim
- Department of Chemistry, Chungnam National University, Daejeon, Republic of Korea.
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Di Sario G, Rossella V, Famulari ES, Maurizio A, Lazarevic D, Giannese F, Felici C. Enhancing clinical potential of liquid biopsy through a multi-omic approach: A systematic review. Front Genet 2023; 14:1152470. [PMID: 37077538 PMCID: PMC10109350 DOI: 10.3389/fgene.2023.1152470] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 03/20/2023] [Indexed: 04/05/2023] Open
Abstract
In the last years, liquid biopsy gained increasing clinical relevance for detecting and monitoring several cancer types, being minimally invasive, highly informative and replicable over time. This revolutionary approach can be complementary and may, in the future, replace tissue biopsy, which is still considered the gold standard for cancer diagnosis. “Classical” tissue biopsy is invasive, often cannot provide sufficient bioptic material for advanced screening, and can provide isolated information about disease evolution and heterogeneity. Recent literature highlighted how liquid biopsy is informative of proteomic, genomic, epigenetic, and metabolic alterations. These biomarkers can be detected and investigated using single-omic and, recently, in combination through multi-omic approaches. This review will provide an overview of the most suitable techniques to thoroughly characterize tumor biomarkers and their potential clinical applications, highlighting the importance of an integrated multi-omic, multi-analyte approach. Personalized medical investigations will soon allow patients to receive predictable prognostic evaluations, early disease diagnosis, and subsequent ad hoc treatments.
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Lubman DM. David M. Lubman-The University of Michigan-A retrospective in research. MASS SPECTROMETRY REVIEWS 2023; 42:643-651. [PMID: 34289523 PMCID: PMC8903096 DOI: 10.1002/mas.21718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/01/2021] [Accepted: 07/02/2021] [Indexed: 06/13/2023]
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Jalaludin I, Lubman DM, Kim J. A guide to mass spectrometric analysis of extracellular vesicle proteins for biomarker discovery. MASS SPECTROMETRY REVIEWS 2023; 42:844-872. [PMID: 34747512 DOI: 10.1002/mas.21749] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 10/21/2021] [Accepted: 10/27/2021] [Indexed: 06/13/2023]
Abstract
Exosomes (small extracellular vesicles) in living organisms play an important role in processes such as cell proliferation or intercellular communication. Recently, exosomes have been extensively investigated for biomarker discoveries for various diseases. An important aspect of exosome analysis involves the development of enrichment methods that have been introduced for successful isolation of exosomes. These methods include ultracentrifugation, size exclusion chromatography, polyethylene glycol-based precipitation, immunoaffinity-based enrichment, ultrafiltration, and asymmetric flow field-flow fractionation among others. To confirm the presence of exosomes, various characterization methods have been utilized such as Western blot analysis, atomic force microscopy, electron microscopy, optical methods, zeta potential, visual inspection, and mass spectrometry. Recent advances in high-resolution separations, high-performance mass spectrometry and comprehensive proteome databases have all contributed to the successful analysis of exosomes from patient samples. Herein we review various exosome enrichment methods, characterization methods, and recent trends of exosome investigations using mass spectrometry-based approaches for biomarker discovery.
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Affiliation(s)
- Iqbal Jalaludin
- Department of Chemistry, Chungnam National University, Daejeon, Republic of Korea
| | - David M Lubman
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, Michigan, USA
| | - Jeongkwon Kim
- Department of Chemistry, Chungnam National University, Daejeon, Republic of Korea
- Graduate School of New Drug Discovery and Development, Chungnam National University, Daejeon, Republic of Korea
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Burton JB, Carruthers NJ, Stemmer PM. Enriching extracellular vesicles for mass spectrometry. MASS SPECTROMETRY REVIEWS 2023; 42:779-795. [PMID: 34632607 DOI: 10.1002/mas.21738] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 09/19/2021] [Accepted: 09/24/2021] [Indexed: 06/13/2023]
Abstract
Extracellular vesicles from plasma, other body fluids and cell culture media hold great promise in the search for biomarkers. Exosomes in particular, the vesicle type that is secreted after being produced in the endocytic pathway and having a diameter of 30-150 nm, are considered to be a conveyance for signaling molecules and, therefore, to hold valuable information regarding the health and activity status of the cells from which they are released. The vesicular nature of exosomes is central to all methods used to separate them from the highly abundant proteins in plasma and other fluids. The enrichment of the vesicles is essential for mass spectrometry-based analysis as they represent only a very small component of all plasma proteins. The progression of isolation techniques for exosomes from ultracentrifugation through chromatographic separation using hydrophobic packing materials shows that effective enrichment is possible and that high throughput approaches to exosome enrichment are achievable.
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Affiliation(s)
- Jordan B Burton
- Institute of Environmental Health Sciences, Wayne State University, Detroit, Michigan, USA
| | | | - Paul M Stemmer
- Institute of Environmental Health Sciences, Wayne State University, Detroit, Michigan, USA
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12
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A review on comparative studies addressing exosome isolation methods from body fluids. Anal Bioanal Chem 2023; 415:1239-1263. [PMID: 35838769 DOI: 10.1007/s00216-022-04174-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/17/2022] [Accepted: 06/10/2022] [Indexed: 12/11/2022]
Abstract
Exosomes emerged as valuable sources of disease biomarkers and new therapeutic tools. However, extracellular vesicles isolation with exosome-like characteristics from certain biofluids is still challenging which can limit their potential use in clinical settings. While ultracentrifugation-based procedures are the gold standard for exosome isolation from cell cultures, no unique and standardized method for exosome isolation from distinct body fluids exists. The complexity, specific composition, and physical properties of each biofluid constitute a technical barrier to obtain reproducible and pure exosome preparations, demanding a detailed characterization of both exosome isolation and characterization methods. Moreover, some isolation procedures can affect downstream proteomic or RNA profiling analysis. This review compiles and discussed a set of comparative studies addressing distinct exosome isolation methods from human biofluids, including cerebrospinal fluid, plasma, serum, saliva, and urine, also focusing on body fluid specific challenges, physical properties, and other potential variation sources. This summarized information will facilitate the choice of exosome isolation methods, based on the type of biological samples available, and hopefully encourage the use of exosomes in translational and clinical research.
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13
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Jalaludin I, Nguyen HQ, Jang KS, Lee J, Lubman DM, Kim J. Matrix-assisted laser desorption/ionization-Fourier-transform ion cyclotron resonance-mass spectrometry analysis of exosomal lipids from human serum. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2023; 37:e9427. [PMID: 36321680 PMCID: PMC9757854 DOI: 10.1002/rcm.9427] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 10/31/2022] [Accepted: 11/01/2022] [Indexed: 06/16/2023]
Abstract
RATIONALE Exosomes contain biomarkers such as proteins and lipids that help in understanding normal physiology and diseases. Lipids, in particular, are infrequently studied using matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) for biomarker discovery. In this study, MALDI was equipped with a high-resolution MS to investigate exosomal lipids from human serum. METHODS Exosomal lipids were profiled using MALDI with Fourier-transform ion cyclotron resonance (FTICR)-MS. Four matrices (i.e., α-cyano-4-hydroxycinnamic acid [CHCA], 2,5-dihydroxybenzoic acid, sinapinic acid, and graphene oxide [GO]) and three sample preparation methods (i.e., dried droplet, thin layer, and two layer) were compared for the number of lipid species detected and the relative abundance of each lipid from human serum and human serum exosomes. RESULTS In sum, 172 and 89 lipid species were identified from human serum and human serum exosomes, respectively, using all the methods. The highest number of exosome lipid species, 69, was detected using the CHCA matrix, whereas only 8 exosome lipid species were identified using the GO matrix. Among the identified lipid species, phosphatidylcholine was identified most frequently, probably due to the use of a positive ion mode. CONCLUSIONS Exosomes and human serum showed comparable lipid profiles as determined using MALDI-FTICR-MS. These findings provide a new perspective on exosomal lipidomics analysis and may serve as a foundation for future lipidomics-based biomarker research using MALDI-FTICR-MS.
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Affiliation(s)
- Iqbal Jalaludin
- Department of Chemistry, Chungnam National University, Daejeon, Republic of Korea
| | - Huu-Quang Nguyen
- Department of Chemistry, Chungnam National University, Daejeon, Republic of Korea
| | - Kyoung-Soon Jang
- Biomedical Omics Center, Korea Basic Science Institute, Cheongju, Republic of Korea
| | - Jaebeom Lee
- Department of Chemistry, Chungnam National University, Daejeon, Republic of Korea
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University, Daejeon, Republic of Korea
| | - David M Lubman
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, Michigan
| | - Jeongkwon Kim
- Department of Chemistry, Chungnam National University, Daejeon, Republic of Korea
- Graduate School of New Drug Discovery and Development, Chungnam National University, Daejeon, Republic of Korea
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14
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Zhu J, Tan Z, Zhang J, An M, Khaykin VM, Cuneo KC, Parikh ND, Lubman DM. Sequential Method for Analysis of CTCs and Exosomes from the Same Sample of Patient Blood. ACS OMEGA 2022; 7:37581-37588. [PMID: 36312392 PMCID: PMC9609053 DOI: 10.1021/acsomega.2c04428] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
Circulating tumor cells (CTCs) and exosomes, both released from the primary tumor into peripheral blood, are a promising source of cancer biomarkers. They are detectable in the blood and carry a large diversity of biological molecules, which can be used for the diagnosis and monitoring of minimally invasive cancers. However, due to their intrinsic differences in counts, size, and molecular contents, studies have focused on only one type of vesicle. Herein, we have developed an integrated system to sequentially isolate CTCs and exosomes from a single patient blood sample for further profiling and analysis. The CTCs are isolated using a commercial filtration method and then the remaining blood is processed using multiple cycles of ultracentrifugation to isolate the exosomes. The method uses two available technologies where the eluent from CTC isolation is usually discarded and interfaces them, so that the eluent can be interfaced to exosome isolation methods. The CTCs are identified based on fluorescence staining of their surface markers, while the exosomes are analyzed using transmission electron microscopy, nanosight tracking analysis, and mass spec proteomic analysis. This analysis showed CTCs detected by their surface markers for metastatic hepatocellular carcinoma (HCC), while essentially none were detected for cirrhosis. The exosome analysis resulted in the identification of ∼500-1000 exosome proteins per sample confirmed by detection of exosome surface markers CD9, CD63, CD81, and TSG101 in addition to proteins related to cancer progression. Proteins enriched in HCC exosomes were shown to be involved in the immune response, metastasis, and proliferation.
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Affiliation(s)
- Jianhui Zhu
- Department
of Surgery, The University of Michigan, 1150 West Medical Center Drive, Ann Arbor, Michigan 48109, United States
| | - Zhijing Tan
- Department
of Surgery, The University of Michigan, 1150 West Medical Center Drive, Ann Arbor, Michigan 48109, United States
| | - Jie Zhang
- Department
of Surgery, The University of Michigan, 1150 West Medical Center Drive, Ann Arbor, Michigan 48109, United States
| | - Mingrui An
- Department
of Surgery, The University of Michigan, 1150 West Medical Center Drive, Ann Arbor, Michigan 48109, United States
| | - Valerie M. Khaykin
- Division
of Gastroenterology and Hepatology, University
of Michigan Medical Center, Ann
Arbor, Michigan 48109, United States
| | - Kyle C. Cuneo
- Department
of Radiation Oncology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Neehar D. Parikh
- Division
of Gastroenterology and Hepatology, University
of Michigan Medical Center, Ann
Arbor, Michigan 48109, United States
| | - David M. Lubman
- Department
of Surgery, The University of Michigan, 1150 West Medical Center Drive, Ann Arbor, Michigan 48109, United States
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15
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Shan L, Gao H, Zhang J, Li W, Su Y, Guo Y. Plasma and serum exosome markers analyzed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry coupled with electron multiplier. Talanta 2022; 247:123560. [PMID: 35623246 DOI: 10.1016/j.talanta.2022.123560] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 05/07/2022] [Accepted: 05/14/2022] [Indexed: 10/18/2022]
Abstract
Although matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a simple, rapid, and high-throughput assay, its microchannel plate (MCP) detector is limited by the low sensitivity and ion saturation effect when analyzing macromolecules. Herein, we introduced a strategy that combined MALDI-TOF MS with electron multiplier (EM) for the direct analysis of exosomal proteins isolated from human plasma and serum. The results demonstrated that EM yielded a higher sensitivity than MCP detector in high-mass range (m/z 5000-100000). Through the analysis of MALDI-TOF MS coupled with EM, chemokine (C-X-C motif) ligand 12 (CXCL12) ion at m/z 7960 and its degradation products at m/z 7927, 7587, and 7553 were identified as characteristic exosomal proteins in plasma. CXCL4 ion at m/z 7765 was identified as a characteristic protein in serum exosomes. Additionally, the peak intensity of CXCL12 and CXCL4 standards exhibited great linear relationship (CXCL12, R2 = 0.989; CXCL4, R2 = 0.986) with the concentrations (ranging from 0.1 to 20 μg/mL) when using EM as detector. In conjunction with ultrasonic assisted matrix coating technology (UAMCT), this assay repeatability in our lab has been excellent with coefficient of variation (CV%) of 4.6% for CXCL12 and 9.3% for CXCL4. Finally, the spectra demonstrated that the intensity of exosome related peaks was significantly enhanced in plasma and serum of patients with Parkinson's disease (PD) (m/z 7553, P < 0.01; m/z 7587, P < 0.01; m/z 7927, P < 0.001; m/z 7980, P < 0.001; m/z 7765, P < 0.01), Alzheimer's disease (AD) (m/z 7553, P < 0.001; m/z 7587, P < 0.001; m/z 7927, P < 0.001; m/z 7980, P < 0.001), and ischemic cerebrovascular disease (ICD) (m/z 7553, P < 0.05; m/z 7587, P < 0.05; m/z 7927, P < 0.01; m/z 7980, P < 0.05; m/z 7765, P < 0.05) compared to that in healthy persons. The fingerprint information of CXCL12 in plasma exosomes has better clinical relevance than serum exosome CXCL4 in MALDI-TOF MS analysis.
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Affiliation(s)
- Liang Shan
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, PR China; National Center for Organic Mass Spectrometry in Shanghai, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 200032, PR China.
| | - Han Gao
- Department of Encephalopathy, Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200071, PR China.
| | - Jing Zhang
- National Center for Organic Mass Spectrometry in Shanghai, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 200032, PR China.
| | - Wentao Li
- Department of Encephalopathy, Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200071, PR China.
| | - Yue Su
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, PR China.
| | - Yinlong Guo
- National Center for Organic Mass Spectrometry in Shanghai, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 200032, PR China.
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16
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Saumell-Esnaola M, Delgado D, García del Caño G, Beitia M, Sallés J, González-Burguera I, Sánchez P, López de Jesús M, Barrondo S, Sánchez M. Isolation of Platelet-Derived Exosomes from Human Platelet-Rich Plasma: Biochemical and Morphological Characterization. Int J Mol Sci 2022; 23:ijms23052861. [PMID: 35270001 PMCID: PMC8911307 DOI: 10.3390/ijms23052861] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 02/25/2022] [Accepted: 03/04/2022] [Indexed: 02/07/2023] Open
Abstract
Platelet-Rich Plasma (PRP) is enriched in molecular messengers with restorative effects on altered tissue environments. Upon activation, platelets release a plethora of growth factors and cytokines, either in free form or encapsulated in exosomes, which have been proven to promote tissue repair and regeneration. Translational research on the potential of exosomes as a safe nanosystem for therapeutic cargo delivery requires standardizing exosome isolation methods along with their molecular and morphological characterization. With this aim, we isolated and characterized the exosomes released by human PRP platelets. Western blot analysis revealed that CaCl2-activated platelets (PLT-Exos-Ca2+) released more exosomes than non-activated ones (PLT-Exos). Moreover, PLT-Exos-Ca2+ exhibited a molecular signature that meets the most up-to-date biochemical criteria for platelet-derived exosomes and possessed morphological features typical of exosomes as assessed by transmission electron microscopy. Array analysis of 105 analytes including growth factors and cytokines showed that PLT-Exos-Ca2+ exhibited lower levels of most analytes compared to PLT-Exos, but relatively higher levels of those consistently validated as components of the protein cargo of platelet exosomes. In summary, the present study provides new insights into the molecular composition of human platelet-derived exosomes and validates a method for isolating highly pure platelet exosomes as a basis for future preclinical studies in regenerative medicine and drug delivery.
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Affiliation(s)
- Miquel Saumell-Esnaola
- Department of Pharmacology, Faculty of Pharmacy, University of the Basque Country UPV/EHU, 01006 Vitoria-Gasteiz, Spain; (M.S.-E.); (M.L.d.J.); (S.B.)
- Bioaraba, Neurofarmacología Celular y Molecular, 01008 Vitoria-Gasteiz, Spain; (G.G.d.C.); (I.G.-B.)
| | - Diego Delgado
- Advanced Biological Therapy Unit, Hospital Vithas Vitoria, 01008 Vitoria-Gasteiz, Spain; (D.D.); (M.B.); (P.S.)
| | - Gontzal García del Caño
- Bioaraba, Neurofarmacología Celular y Molecular, 01008 Vitoria-Gasteiz, Spain; (G.G.d.C.); (I.G.-B.)
- Department of Neurosciences, Faculty of Pharmacy, University of the Basque Country UPV/EHU, 01006 Vitoria-Gasteiz, Spain
| | - Maider Beitia
- Advanced Biological Therapy Unit, Hospital Vithas Vitoria, 01008 Vitoria-Gasteiz, Spain; (D.D.); (M.B.); (P.S.)
| | - Joan Sallés
- Department of Pharmacology, Faculty of Pharmacy, University of the Basque Country UPV/EHU, 01006 Vitoria-Gasteiz, Spain; (M.S.-E.); (M.L.d.J.); (S.B.)
- Bioaraba, Neurofarmacología Celular y Molecular, 01008 Vitoria-Gasteiz, Spain; (G.G.d.C.); (I.G.-B.)
- Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), 28029 Madrid, Spain
- Correspondence: (J.S.); (M.S.); Tel.: +34-945-013114 (J.S.); +34-945-252077 (M.S.)
| | - Imanol González-Burguera
- Bioaraba, Neurofarmacología Celular y Molecular, 01008 Vitoria-Gasteiz, Spain; (G.G.d.C.); (I.G.-B.)
- Department of Neurosciences, Faculty of Pharmacy, University of the Basque Country UPV/EHU, 01006 Vitoria-Gasteiz, Spain
| | - Pello Sánchez
- Advanced Biological Therapy Unit, Hospital Vithas Vitoria, 01008 Vitoria-Gasteiz, Spain; (D.D.); (M.B.); (P.S.)
| | - Maider López de Jesús
- Department of Pharmacology, Faculty of Pharmacy, University of the Basque Country UPV/EHU, 01006 Vitoria-Gasteiz, Spain; (M.S.-E.); (M.L.d.J.); (S.B.)
- Bioaraba, Neurofarmacología Celular y Molecular, 01008 Vitoria-Gasteiz, Spain; (G.G.d.C.); (I.G.-B.)
| | - Sergio Barrondo
- Department of Pharmacology, Faculty of Pharmacy, University of the Basque Country UPV/EHU, 01006 Vitoria-Gasteiz, Spain; (M.S.-E.); (M.L.d.J.); (S.B.)
- Bioaraba, Neurofarmacología Celular y Molecular, 01008 Vitoria-Gasteiz, Spain; (G.G.d.C.); (I.G.-B.)
- Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), 28029 Madrid, Spain
| | - Mikel Sánchez
- Advanced Biological Therapy Unit, Hospital Vithas Vitoria, 01008 Vitoria-Gasteiz, Spain; (D.D.); (M.B.); (P.S.)
- Arthroscopic Surgery Unit, Hospital Vithas Vitoria, 01008 Vitoria-Gasteiz, Spain
- Correspondence: (J.S.); (M.S.); Tel.: +34-945-013114 (J.S.); +34-945-252077 (M.S.)
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17
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Zheng H, Zhao J, Wang X, Yan S, Chu H, Gao M, Zhang X. Integrated Pipeline of Rapid Isolation and Analysis of Human Plasma Exosomes for Cancer Discrimination Based on Deep Learning of MALDI-TOF MS Fingerprints. Anal Chem 2022; 94:1831-1839. [PMID: 35025210 DOI: 10.1021/acs.analchem.1c04762] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Plasma exosomes have shown great potential for liquid biopsy in clinical cancer diagnosis. Herein, we present an integrated strategy for isolating and analyzing exosomes from human plasma rapidly and then discriminating different cancers excellently based on deep learning fingerprints of plasma exosomes. Sequential size-exclusion chromatography (SSEC) was developed efficiently for separating exosomes from human plasma. SSEC isolated plasma exosomes, taking as less as 2 h for a single sample with high purity such that the discard rates of high-density lipoproteins and low/very low-density lipoproteins were 93 and 85%, respectively. Benefitting from the rapid and high-purity isolation, the contents encapsulated in exosomes, covered by plasma proteins, were well profiled by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MS). We further analyzed 220 clinical samples, including 79 breast cancer patients, 57 pancreatic cancer patients, and 84 healthy controls. After MS data pre-processing and feature selection, the extracted MS feature peaks were utilized as inputs for constructing a multi-classifier artificial neural network (denoted as Exo-ANN) model. The optimized model avoided overfitting and performed well in both training cohorts and test cohorts. For the samples in the independent test cohort, it realized a diagnosed accuracy of 80.0% with an area under the curve of 0.91 for the whole group. These results suggest that our integrated pipeline may become a generic tool for liquid biopsy based on the analysis of plasma exosomes in clinics.
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Affiliation(s)
- Haoyang Zheng
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
| | - Jiandong Zhao
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Shanghai 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Xuantang Wang
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
| | - Shaohan Yan
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
| | - Huimin Chu
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
| | - Mingxia Gao
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
| | - Xiangmin Zhang
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
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18
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Nguyen MCT, Nguyen HQ, Jang H, Noh S, Lee SY, Jang KS, Lee J, Sohn Y, Yee K, Jung H, Kim J. Sterilization effects of UV laser irradiation on Bacillus atrophaeus spore viability, structure, and proteins. Analyst 2021; 146:7682-7692. [PMID: 34812439 DOI: 10.1039/d1an01717a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Bacillus spores are highly resistant to toxic chemicals and extreme environments. Because some Bacillus species threaten public health, spore inactivation techniques have been intensively investigated. We exposed Bacillus atrophaeus spores to a 266 nm Nd:YVO4 laser at a laser power of 1 W and various numbers of scans. As a result, the UV laser reduced the viability of Bacillus atrophaeus spores. Although the outer coat of spores remained intact after UV laser irradiation of 720 scans, damage inside the spores was observed. Spore proteins were identified by matrix-assisted laser desorption/ionization Fourier transform ion cyclotron resonance mass spectrometry during the course of UV laser irradiation. Photochemical and photothermal processes are believed to be involved in the UV laser sterilization of Bacillus spores. Our findings suggest that a UV laser is capable of sterilizing Bacillus atrophaeus spores.
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Affiliation(s)
- My-Chi Thi Nguyen
- Department of Chemistry, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Huu-Quang Nguyen
- Department of Chemistry, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Hanbyeol Jang
- Department of Chemistry, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Sojung Noh
- Department of Chemistry, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Seong-Yeon Lee
- Department of Physics and Institute of Quantum Systems, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Kyoung-Soon Jang
- Biomedical Omics Center, Korea Basic Science Institute, Cheongju, Republic of Korea
| | - Jaebeom Lee
- Department of Chemistry, Chungnam National University, Daejeon, 34134, Republic of Korea.,Department of Chemical Engineering and Applied Chemistry, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Youngku Sohn
- Department of Chemistry, Chungnam National University, Daejeon, 34134, Republic of Korea.,Department of Chemical Engineering and Applied Chemistry, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Kiju Yee
- Department of Physics and Institute of Quantum Systems, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Heesoo Jung
- Chem-Bio Technology Center, Agency for Defense Development (ADD), Yuseong P.O. Box 35, Daejeon, 34186, Republic of Korea.
| | - Jeongkwon Kim
- Department of Chemistry, Chungnam National University, Daejeon, 34134, Republic of Korea.,Graduate School of New Drug Discovery and Development, Chungnam National University, Daejeon, Republic of Korea.
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19
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Lippold S, Thavarajah R, Reusch D, Wuhrer M, Nicolardi S. Glycoform analysis of intact erythropoietin by MALDI FT-ICR mass spectrometry. Anal Chim Acta 2021; 1185:339084. [PMID: 34711323 DOI: 10.1016/j.aca.2021.339084] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 09/13/2021] [Accepted: 09/19/2021] [Indexed: 10/20/2022]
Abstract
Recombinant human erythropoietin (EPO) is a complex therapeutic glycoprotein with three N- and one O-glycosylation sites. Glycosylation of EPO influences its safety and efficacy and is defined as a critical quality attribute. Thus, analytical methods for profiling EPO glycosylation are highly demanded. Owing to the complexity of the intact protein, information about EPO glycosylation is commonly derived from released glycan and glycopeptide analysis using mass spectrometry (MS). Alternatively, comprehensive insights into the glycoform heterogeneity of intact EPO are obtained using ESI MS-based methods with or without upfront separation of EPO glycoforms. MALDI MS, typically performed with TOF mass analyzers, has been also used for the analysis of intact EPO but, due to the poor glycoform resolution, has only provided limited glycoform information. Here, we present a MALDI FT-ICR MS method for the glycosylation profiling of intact EPO with improved glycoform resolution and without loss of sialic acid residues commonly observed in MALDI analysis. Three EPO variants were characterized in-depth and up to 199 glycoform compositions were assigned from the evaluation of doubly-charged ions, without any deconvolution of the mass spectra. Key glycosylation features such as sialylation, acetylation, and N-acetyllactosamine repeats were determined and found to agree with previously reported data obtained from orthogonal analyses. The developed method allowed for a fast and straightforward data acquisition and evaluation and can be potentially used for the high-throughput comparison of EPO samples throughout its manufacturing process.
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Affiliation(s)
- Steffen Lippold
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands.
| | - Raashina Thavarajah
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
| | - Dietmar Reusch
- Pharma Technical Development Penzberg, Roche Diagnostics GmbH, Penzberg, Germany
| | - Manfred Wuhrer
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
| | - Simone Nicolardi
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands.
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20
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Han Z, Yi J, Yang Y, Li D, Peng C, Long S, Peng X, Shen Y, Liu B, Qiao L. SERS and MALDI-TOF MS based plasma exosome profiling for rapid detection of osteosarcoma. Analyst 2021; 146:6496-6505. [PMID: 34569564 DOI: 10.1039/d1an01163d] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Osteosarcoma is the most frequent primary bone cancer, particularly among children and adolescents. The early diagnosis of osteosarcoma is significant for timely clinical treatment to reduce the mortality of patients. Exosomes play a significant role in intercellular communication and serve as promising biomarkers in liquid biopsy for the diagnosis and monitoring of tumors. Herein, we report the utility of surface-enhanced Raman scattering (SERS) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) for rapid identification of osteosarcoma. We firstly profiled the intrinsic SERS signals and MALDI-TOF mass fingerprints of different subgroups of extracellular vesicles (EVs) and the corresponding cells, demonstrating that the SERS signals and MALDI-TOF mass spectra of exosomes from different types of cells were more discriminative compared to those of large and medium EVs and the cells themselves. Then, we characterized plasma-derived exosomes of 15 osteosarcoma patients and 15 healthy volunteers using SERS and MALDI-TOF MS, revealing distinctive biochemical differences in the spectra. We further utilized a data fusion approach to combine the two types of spectroscopic techniques, differentiating osteosarcoma patients from healthy controls with higher precision than either technique. The results reveal that the non-invasive liquid biopsy method using SERS and MALDI-TOF MS fingerprinting of exosomes has great potential for rapid diagnosis of osteosarcoma.
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Affiliation(s)
- Zhenzhen Han
- Department of Chemistry, and Shanghai Stomatological Hospital, Fudan University, Shanghai 200000, China.
| | - Jia Yi
- Department of Chemistry, and Shanghai Stomatological Hospital, Fudan University, Shanghai 200000, China.
| | - Yi Yang
- Department of Chemistry, and Shanghai Stomatological Hospital, Fudan University, Shanghai 200000, China.
| | - Dandan Li
- Department of Chemistry, and Shanghai Stomatological Hospital, Fudan University, Shanghai 200000, China.
| | - Cheng Peng
- Department of Orthopedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200000, China
| | - Shuping Long
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai, China
| | - Xinyan Peng
- Department of Chemistry, and Shanghai Stomatological Hospital, Fudan University, Shanghai 200000, China.
| | - Yuhui Shen
- Department of Orthopedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200000, China
| | - Baohong Liu
- Department of Chemistry, and Shanghai Stomatological Hospital, Fudan University, Shanghai 200000, China.
| | - Liang Qiao
- Department of Chemistry, and Shanghai Stomatological Hospital, Fudan University, Shanghai 200000, China.
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21
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Gao X, Teng X, Dai Y, Li J. Rolling Circle Amplification-Assisted Flow Cytometry Approach for Simultaneous Profiling of Exosomal Surface Proteins. ACS Sens 2021; 6:3611-3620. [PMID: 34632781 DOI: 10.1021/acssensors.1c01163] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Exosomes that carry multiple proteins from the originating cells are known as emerging biomarkers for tumor diagnostics. However, it is still technically challenging to accurately evaluate subtle differences of exosomal membrane proteins. Here, we developed a rolling circle amplification (RCA)-assisted flow cytometry approach (FCA) to simultaneously profile surface proteins and quantify exosomes. In this work, specific anti-CD63 antibody-conjugated magnetic beads were first utilized to capture exosomes. Then, the captured exosomes were bound with DNA primers, which comprise exosomal surface protein-specific recognition aptamers. The RCA reaction generates repeat DNA sequences for fluorescent probe hybridization. Finally, a conventional flow cytometer was introduced to phenotype exosomal protein markers. Such a sensitive RCA-assisted FCA displays an excellent detection limit of 1.3 × 105 exosome/mL. The variable composition of four protein markers on different cell-derived exosomes was sensitively detected through changing the protein-recognition sequence of the DNA primer, which reveals a heterogeneous pattern. Exosomes from different cell sources could be distinguished by the abundance difference of multiple surface proteins. Furthermore, the developed RCA-assisted FCA enabled quantitative analysis of blood samples from lung cancer patients, indicating its potential for early clinical diagnosis and prognosis of cancer.
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Affiliation(s)
- Xiaoyi Gao
- Department of Chemistry, Center for BioAnalytical Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
| | - Xucong Teng
- Department of Chemistry, Center for BioAnalytical Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
| | - Yicong Dai
- Department of Chemistry, Center for BioAnalytical Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
| | - Jinghong Li
- Department of Chemistry, Center for BioAnalytical Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
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22
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Hu J, Liu F, Chen Y, Shangguan G, Ju H. Mass Spectrometric Biosensing: A Powerful Approach for Multiplexed Analysis of Clinical Biomolecules. ACS Sens 2021; 6:3517-3535. [PMID: 34529414 DOI: 10.1021/acssensors.1c01394] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Rapid and sensitive detection of clinical biomolecules in a multiplexed fashion is of great importance for accurate diagnosis of diseases. Mass spectrometric (MS) approaches are exceptionally suitable for clinical analysis due to its high throughput, high sensitivity, and reliable qualitative and quantitative capabilities. To break through the bottleneck of MS technique for detecting high-molecular-weight substances with low ionization efficiency, the concept of mass spectrometric biosensing has been put forward by adopting mass spectrometric chips to recognize the targets and mass spectrometry to detect the signals switched by the recognition. In this review, the principle of mass spectrometric sensing, the construction of different mass tags used for biosensing, and the typical combination mode of mass spectrometric imaging (MSI) technique are summarized. Future perspectives including the design of portable matching platforms, exploitation of novel mass tags, development of effective signal amplification strategies, and standardization of MSI methodologies are proposed to promote the advancements and practical applications of mass spectrometric biosensing.
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Affiliation(s)
- Junjie Hu
- College of Forensic Medicine and Laboratory Medicine, Jining Medical University, Jining 272067, China
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Fei Liu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Yunlong Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Guoqiang Shangguan
- College of Forensic Medicine and Laboratory Medicine, Jining Medical University, Jining 272067, China
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
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23
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Han Z, Peng C, Yi J, Wang Y, Liu Q, Yang Y, Long S, Qiao L, Shen Y. Matrix-assisted laser desorption ionization mass spectrometry profiling of plasma exosomes evaluates osteosarcoma metastasis. iScience 2021; 24:102906. [PMID: 34401680 PMCID: PMC8355924 DOI: 10.1016/j.isci.2021.102906] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 06/08/2021] [Accepted: 07/21/2021] [Indexed: 12/12/2022] Open
Abstract
Osteosarcoma is the most common primary sarcoma of bone among adolescents, often characterized by early lung metastasis resulting in high mortality. Recently, exosomes have been used in liquid biopsy to monitor tumors. Herein, we used matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to profile human plasma exosomes for the evaluation of osteosarcoma lung metastasis. Forty patients with osteosarcoma with (n = 20) or without (n = 20) lung metastasis as well as 12 heathy controls were recruited. Exosomes were isolated from human plasma for MALDI-TOF MS analysis. Multivariate statistical analyses were performed based on the MALDI-TOF mass spectra. The strategy can efficiently differentiate osteosarcomas from healthy controls and further discriminate osteosarcoma lung metastasis from non-lung metastasis. We identified seven exosomal proteins as potential biomarkers of osteosarcoma lung metastasis. The proposed method holds great promise to clinically diagnose osteosarcoma and monitor osteosarcoma lung metastasis.
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Affiliation(s)
- Zhenzhen Han
- Department of Orthopedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200000, China
- Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Cheng Peng
- Department of Orthopedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200000, China
| | - Jia Yi
- Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Yiwen Wang
- Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Qi Liu
- Department of Orthopedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200000, China
| | - Yi Yang
- Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Shuping Long
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai, China
| | - Liang Qiao
- Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Yuhui Shen
- Department of Orthopedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200000, China
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24
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Yu Z, Zhao C, Hu S, Zhang H, Li W, Zhang R, Luo Q, Yang H. MALDI-MS-based biomarker analysis of extracellular vesicles from human lung carcinoma cells. RSC Adv 2021; 11:25375-25380. [PMID: 35478925 PMCID: PMC9037017 DOI: 10.1039/d1ra04305f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 07/12/2021] [Indexed: 12/19/2022] Open
Abstract
Extracellular vesicles (EVs) are actively secreted by mammalian cells. They are increasingly recognized as promising circulating biomarkers of disease progression. Matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) is currently one of the most powerful techniques for the rapid analysis of biological samples, especially for discovering biomarkers for disease diagnosis and prognosis. It is unclear what cell culture medium components and EV isolation methods are suitable for MALDI-TOF MS analysis. Using a human lung carcinoma cell line (A549), we investigated and optimized the critical experimental conditions for EVs' protein profiling by combining differential ultracentrifugation and MALDI-TOF MS. The results demonstrated that medium components and ultracentrifugation procedures to extract EVs played important roles in MS detection. Compared with EV-depleted serum and normal serum medium, conditioned medium with 2% fetal bovine serum in this study maintained cell proliferation and displayed significant protein profiling of EVs. RPS27A (ribosomal protein), which plays an essential role in mRNA translation and ribosome assembly for the differentiation of cancer cells, was detected from the EVs of lung cancer cells associated with cancer cell migration and invasion. We also found the known tumor diagnosis marker, which is S100A10_S100 calcium-binding protein A10. Therefore, MALDI-TOF MS-based EV analysis with optimized experimental protocols can contribute to future development of rapid screening techniques of protein biomarkers associated with early cancer diagnosis.
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Affiliation(s)
- Zitong Yu
- Bionic Sensing and Intelligence Center, Institute of Biomedical and Health Engineering, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences Shenzhen 518055 China
| | - Chao Zhao
- Bionic Sensing and Intelligence Center, Institute of Biomedical and Health Engineering, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences Shenzhen 518055 China
| | - Shi Hu
- Bionic Sensing and Intelligence Center, Institute of Biomedical and Health Engineering, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences Shenzhen 518055 China
| | - Huitao Zhang
- Research Center for Medical Artificial Intelligence, Institute of Biomedical and Health Engineering, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences Shenzhen 518055 China
| | - Wenbo Li
- Bionic Sensing and Intelligence Center, Institute of Biomedical and Health Engineering, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences Shenzhen 518055 China
| | - Renjie Zhang
- Bionic Sensing and Intelligence Center, Institute of Biomedical and Health Engineering, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences Shenzhen 518055 China
| | - Qian Luo
- Bionic Sensing and Intelligence Center, Institute of Biomedical and Health Engineering, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences Shenzhen 518055 China
| | - Hui Yang
- Bionic Sensing and Intelligence Center, Institute of Biomedical and Health Engineering, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences Shenzhen 518055 China .,CAS Key Laboratory of Health Informatics, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences Shenzhen 518055 China
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25
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Nguyen HQ, Lee D, Kim Y, Bang G, Cho K, Lee YS, Yeon JE, Lubman DM, Kim J. Label-free quantitative proteomic analysis of serum extracellular vesicles differentiating patients of alcoholic and nonalcoholic fatty liver diseases. J Proteomics 2021; 245:104278. [PMID: 34089894 DOI: 10.1016/j.jprot.2021.104278] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 04/28/2021] [Accepted: 05/30/2021] [Indexed: 02/07/2023]
Abstract
Alcoholic liver disease (ALD) and nonalcoholic fatty liver disease (NAFLD) are typically asymptomatic and slow-progressing but potentially fatal diseases that are common causes of liver cirrhosis and related complications. Exosomes are nano-sized extracellular vesicles that have been linked to various intercellular communication processes and can carry biological materials reflecting the state and severity of disease. In this study, shotgun proteomic analysis of the protein expression profiles of extracellular vesicles, including exosomes and microvesicles, enriched from human serum samples of 24 patients diagnosed with various fatty liver diseases was performed using liquid chromatography tandem mass spectrometry (LC-MS/MS) followed by protein identification and label-free quantification using the MaxQuant platform. A total of 329 proteins, including 190 previously reported exosome-specific proteins, were identified from four types of liver disease, where significant differences in protein expression were found in apolipoproteins, immunoglobulins, and other previously reported markers of liver disease. Principal component analysis of 61 proteins identified from MaxQuant analysis of the LC-MS/MS data provided a confident differentiation between ALD and NAFLD. SIGNIFICANCE: The current investigation revealed the difference among various types of liver disease using LC-MS/MS of exosomes enriched from human serum samples of 24 patients where the most significantly up-regulation proteins were alpha-2-macroglobulin for alcoholic hepatitis and apolipoprotein C3 for nonalcoholic fatty liver disease.
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Affiliation(s)
- Huu-Quang Nguyen
- Department of Chemistry, Chungnam National University, Daejeon, Republic of Korea
| | - Dabin Lee
- Department of Chemistry, Chungnam National University, Daejeon, Republic of Korea
| | - Yeoseon Kim
- Department of Chemistry, Chungnam National University, Daejeon, Republic of Korea
| | - Geul Bang
- Research Center of Bioconvergence Analysis, Korea Basic Science Institute, Ochang, Republic of Korea
| | - Kun Cho
- Research Center of Bioconvergence Analysis, Korea Basic Science Institute, Ochang, Republic of Korea
| | - Young-Sun Lee
- Department of Internal Medicine, Korea University College of Medicine, Seoul, Republic of Korea
| | - Jong Eun Yeon
- Department of Internal Medicine, Korea University College of Medicine, Seoul, Republic of Korea
| | - David M Lubman
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, MI, USA
| | - Jeongkwon Kim
- Department of Chemistry, Chungnam National University, Daejeon, Republic of Korea; Graduate School of New Drug Discovery and Development, Chungnam National University, Daejeon, Republic of Korea.
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26
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Srivatsav AT, Kapoor S. The Emerging World of Membrane Vesicles: Functional Relevance, Theranostic Avenues and Tools for Investigating Membrane Function. Front Mol Biosci 2021; 8:640355. [PMID: 33968983 PMCID: PMC8101706 DOI: 10.3389/fmolb.2021.640355] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 01/26/2021] [Indexed: 12/12/2022] Open
Abstract
Lipids are essential components of cell membranes and govern various membrane functions. Lipid organization within membrane plane dictates recruitment of specific proteins and lipids into distinct nanoclusters that initiate cellular signaling while modulating protein and lipid functions. In addition, one of the most versatile function of lipids is the formation of diverse lipid membrane vesicles for regulating various cellular processes including intracellular trafficking of molecular cargo. In this review, we focus on the various kinds of membrane vesicles in eukaryotes and bacteria, their biogenesis, and their multifaceted functional roles in cellular communication, host-pathogen interactions and biotechnological applications. We elaborate on how their distinct lipid composition of membrane vesicles compared to parent cells enables early and non-invasive diagnosis of cancer and tuberculosis, while inspiring vaccine development and drug delivery platforms. Finally, we discuss the use of membrane vesicles as excellent tools for investigating membrane lateral organization and protein sorting, which is otherwise challenging but extremely crucial for normal cellular functioning. We present current limitations in this field and how the same could be addressed to propel a fundamental and technology-oriented future for extracellular membrane vesicles.
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Affiliation(s)
- Aswin T. Srivatsav
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, India
| | - Shobhna Kapoor
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, India
- Wadhwani Research Center of Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
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27
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Yan H, Li Y, Cheng S, Zeng Y. Advances in Analytical Technologies for Extracellular Vesicles. Anal Chem 2021; 93:4739-4774. [PMID: 33635060 DOI: 10.1021/acs.analchem.1c00693] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- He Yan
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Yutao Li
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Shibo Cheng
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Yong Zeng
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States.,University of Florida Health Cancer Center, Gainesville, Florida 32610, United States
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28
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Xue VW, Yang C, Wong SCC, Cho WCS. Proteomic profiling in extracellular vesicles for cancer detection and monitoring. Proteomics 2021; 21:e2000094. [PMID: 33665903 DOI: 10.1002/pmic.202000094] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 02/24/2021] [Accepted: 03/02/2021] [Indexed: 12/12/2022]
Abstract
Extracellular vesicles (EVs) are nanometer-size lipid vesicles released by cells, which play essential biological functions in intercellular communication. Increasing evidence indicates that EVs participate in cancer development, including invasion, migration, metastasis, and cancer immune modulation. One of the key mechanisms is that EVs affect different cells in the tumor microenvironment through surface-anchor proteins and protein cargos. Moreover, proteins specifically expressed in tumor-derived EVs can be applied in cancer diagnosis and monitoring. Besides, the EV proteome also helps to understand drug resistance in cancers and to guide clinical medication. With the development of mass spectrometry and array-based multi-protein detection, the research of EV proteomics has entered a new era. The high-throughput parallel proteomic profiling based on these new platforms allows us to study the impact of EV proteome on cancer progression more comprehensively and to describe the proteomic landscape in cancers with more details. In this article, we review the role and function of different types of EVs in cancer progression. More importantly, we summarize the proteomic profiling of EVs based on different methods and the application of EV proteome in cancer detection and monitoring.
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Affiliation(s)
- Vivian Weiwen Xue
- School of Basic Medical Sciences, Shenzhen University Health Science Centre, Shenzhen University, Shenzhen, China
| | - Chenxi Yang
- School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Sze Chuen Cesar Wong
- Faculty of Health and Social Sciences, Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong SAR, China
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29
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Fasih Ramandi N, Faranoush M, Ghassempour A, Aboul-Enein HY. Mass Spectrometry: A Powerful Method for Monitoring Various Type of Leukemia, Especially MALDI-TOF in Leukemia's Proteomics Studies Review. Crit Rev Anal Chem 2021; 52:1259-1286. [PMID: 33499652 DOI: 10.1080/10408347.2021.1871844] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Recent success in studying the proteome, as a source of biomarkers, has completely changed our understanding of leukemia (blood cancer). The identification of differentially expressed proteins, such as relapse and drug resistance proteins involved in leukemia by using various ionization sources and mass analyzers of mass spectrometry techniques, has helped scientists find better diagnosis, prognosis, and treatment strategies. With the aid of this powerful analytical technique, we can investigate the qualification/quantification of proteins, protein-protein interactions, post-translational modifications, and find the correlation between proteins and their genes with the hope of finding the missing parts of the successful therapy puzzle. In this review, we followed different MS sources and analyzers which used for monitoring various type of leukemia, then focused on MALDI-TOF MS as a quick and reliable method for studying proteins. Due to several review published for other techniques, the present review is the first work in this field. Also, by classifying more than 400 proteins, we have found 42 proteins are involved in two or three different stages of leukemia. Finally, we have suggested six specific biomarkers for AML, one for ALL, three biomarkers with a role in the etiology of leukemia and 13 markers with the potential for further studies.
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Affiliation(s)
- Negin Fasih Ramandi
- Medicinal Plants and Drugs Research Institute, Shahid Beheshti University, Tehran, Iran
| | - Mohammad Faranoush
- Pediatric Growth and Development Research Center, Institute of Endocrinology, Iran University of Medical Sciences, Tehran, Iran
| | - Alireza Ghassempour
- Medicinal Plants and Drugs Research Institute, Shahid Beheshti University, Tehran, Iran
| | - Hassan Y Aboul-Enein
- Pharmaceutical and Medicinal Chemistry Department, Pharmaceutical and Drug Industries Research Division, National Research Center, Cairo, Egypt
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30
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Wang Y, Zhang K, Huang X, Qiao L, Liu B. Mass Spectrometry Imaging of Mass Tag Immunoassay Enables the Quantitative Profiling of Biomarkers from Dozens of Exosomes. Anal Chem 2020; 93:709-714. [PMID: 33315384 DOI: 10.1021/acs.analchem.0c03904] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Yuning Wang
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai 200438, China
| | - Kun Zhang
- Department of Neurosurgery, Shanghai Children’s Hospital, Shanghai Jiao Tong University, Shanghai 200062, China
| | - Xuedong Huang
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai 200438, China
| | - Liang Qiao
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai 200438, China
| | - Baohong Liu
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai 200438, China
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31
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Xing Y, Cheng Z, Wang R, Lv C, James TD, Yu F. Analysis of extracellular vesicles as emerging theranostic nanoplatforms. Coord Chem Rev 2020. [DOI: 10.1016/j.ccr.2020.213506] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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32
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de Boer C, Calder B, Blackhurst D, Marais D, Blackburn J, Steinmaurer M, Woudberg NJ, Lecour S, Lovett J, Myburgh K, Bezuidenhout D, Human P, Davies NH. Analysis of the regenerative capacity of human serum exosomes after a simple multistep separation from lipoproteins. J Tissue Eng Regen Med 2020; 15:63-77. [PMID: 33175463 DOI: 10.1002/term.3155] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/08/2020] [Accepted: 10/19/2020] [Indexed: 01/03/2023]
Abstract
Due to the abundance of lipoproteins in blood, it is challenging to characterize the biological functions and components of blood-derived extracellular vesicles. The aim of this study was to develop a multiple-step purification protocol to separate serum exosomes from serum proteins and lipoproteins and assess their regenerative potential. Exosomes were isolated by concentrating them in human serum using ultracentrifugation (UC), followed sequentially by density gradient (DG) UC and size exclusion chromatography (SEC). Purity and characterization were assessed by western blots, Lipoprint®, enzyme-linked immunosorbent assay, electron microscopy, mass spectrometry, and nanoparticle tracking analysis. Functionality was assessed by cell proliferation analysis and with an in vivo subcutaneous angiogenesis model. SEC alone isolated nano-sized vesicles possessing vesicle markers TSG101 and CD9, but there was a substantial presence of apolipoprotein B, predominantly derived from very-low- and intermediate-density lipoprotein particles. This was reduced to an undetectable level using the combined UC DG SEC approach. Mass spectrometry identified 224 proteins in UC DG SEC isolates relative to the 135 from SEC, with considerable increases in exosome-related proteins and reductions in lipoproteins. A consistent but limited increase in human dermal fibroblast proliferation and evidence of neovascularization enhancement were observed after exposure to UC DG SEC exosomes. An UC DG SEC purification protocol considerably improved the removal of lipoproteins during isolation of serum exosomes. The purified exosomes stimulated cell proliferation and potentially increased an in vivo angiogenic response. This multistep purification allows for more accurate identification of serum exosome functional activity and composition.
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Affiliation(s)
- Candice de Boer
- Cardiovascular Research Unit, Department of Surgery, University of Cape Town, Observatory, South Africa
| | - Bridget Calder
- Division of Chemical & Systems Biology, Department of Integrative Biomedical Sciences, Institute of Infectious Disease & Molecular Medicine, University of Cape Town, Observatory, South Africa
| | - Dee Blackhurst
- Division of Chemical Pathology, Department of Pathology, University of Cape Town, Observatory, South Africa
| | - David Marais
- Division of Chemical Pathology, Department of Pathology, University of Cape Town, Observatory, South Africa
| | - Jonathan Blackburn
- Division of Chemical & Systems Biology, Department of Integrative Biomedical Sciences, Institute of Infectious Disease & Molecular Medicine, University of Cape Town, Observatory, South Africa
| | - Martina Steinmaurer
- Cardiovascular Research Unit, Department of Surgery, University of Cape Town, Observatory, South Africa
| | - Nicholas J Woudberg
- Department of Medicine, Hatter Institute for Cardiovascular Research in Africa, University of Cape Town, Observatory, South Africa
| | - Sandrine Lecour
- Department of Medicine, Hatter Institute for Cardiovascular Research in Africa, University of Cape Town, Observatory, South Africa
| | - Jason Lovett
- Department of Physiological Sciences, Stellenbosch University, Stellenbosch, South Africa
| | - Kathy Myburgh
- Department of Physiological Sciences, Stellenbosch University, Stellenbosch, South Africa
| | - Deon Bezuidenhout
- Cardiovascular Research Unit, Department of Surgery, University of Cape Town, Observatory, South Africa
| | - Paul Human
- Cardiovascular Research Unit, Department of Surgery, University of Cape Town, Observatory, South Africa
| | - Neil H Davies
- Cardiovascular Research Unit, Department of Surgery, University of Cape Town, Observatory, South Africa
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33
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Mallia A, Gianazza E, Zoanni B, Brioschi M, Barbieri SS, Banfi C. Proteomics of Extracellular Vesicles: Update on Their Composition, Biological Roles and Potential Use as Diagnostic Tools in Atherosclerotic Cardiovascular Diseases. Diagnostics (Basel) 2020; 10:diagnostics10100843. [PMID: 33086718 PMCID: PMC7588996 DOI: 10.3390/diagnostics10100843] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/13/2020] [Accepted: 10/16/2020] [Indexed: 02/07/2023] Open
Abstract
Extracellular vesicles (EVs) are lipid-bound vesicles released from cells under physiological and pathological conditions. Basing on biogenesis, dimension, content and route of secretion, they can be classified into exosomes, microvesicles (MVs) and apoptotic bodies. EVs have a key role as bioactive mediators in intercellular communication, but they are also involved in other physiological processes like immune response, blood coagulation, and tissue repair. The interest in studying EVs has increased over the years due to their involvement in several diseases, such as cardiovascular diseases (CVDs), and their potential role as biomarkers in diagnosis, therapy, and in drug delivery system development. Nowadays, the improvement of mass spectrometry (MS)-based techniques allows the characterization of the EV protein composition to deeply understand their role in several diseases. In this review, a critical overview is provided on the EV’s origin and physical properties, as well as their emerging functional role in both physiological and disease conditions, focusing attention on the role of exosomes in CVDs. The most important cardiac exosome proteomic studies will be discussed giving a qualitative and quantitative characterization of the exosomal proteins that could be used in future as new potential diagnostic markers or targets for specific therapies.
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34
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Zhang T, Hu L, Ma H, Ni F, Liu F, Chen H. Detection of Tear Components Using Matrix-Assisted Laser Desorption Ionization/Time-of-Flight Mass Spectrometry for Rapid Dry Eye Diagnosis. J Proteome Res 2020; 19:3644-3651. [PMID: 32786892 DOI: 10.1021/acs.jproteome.0c00138] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The tear is a biological fluid that has the diagnostic potential for ocular diseases. Extracellular vesicles (EVs), widly detected in various biofluids including tears, are nanoparticles released by living cells and considered as promising detection sources for noninvasive liquid biopsy. Understanding the roles of tears and tear-EVs in ocular diseases such as dry eye can facilitate the studies of clinical diagnosis, which usually entails detecting such liquid objects with a rapid and effective method. In this study, we used a mass spectrometry-based strategy to analyze peptidome/proteome profiles of tears and EVs for rapid dry eye diagnosis. Nanosized EVs were isolated from tears of both healthy control (HC) individuals and dry eye syndrome (DES) patients, and the tear compositions were further analyzed by tracking their fingerprints with matrix-assisted laser desorption ionization/time-of-flight mass spectrometry. The fingerprints of tear-EVs could be observed in a dose-dependent manner and tears, allowing for comparison of the discriminant peaks between tears and EVs. By analyzing these peaks, the fingerprints of both tear and tear-EVs were showed to have the capability of distinguishing patients with DES from HC donors and providing an efficient way for screening potential DES biomarkers. The proposed tear and EV fingerprinting approach is expected to be a potential tool in the rapid diagnosis of ocular diseases and in-depth research on pathogenesis. Data are available via ProteomeXchange with identifier PXD020217.
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Affiliation(s)
- Ting Zhang
- School of Ophthalmology & Optometry, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Liang Hu
- School of Ophthalmology & Optometry, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Huixiang Ma
- School of Ophthalmology & Optometry, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Fangfang Ni
- School of Ophthalmology & Optometry, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Fei Liu
- School of Ophthalmology & Optometry, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China.,Wenzhou Institute, University of Chinese Academy of Science, Wenzhou, Zhejiang 325001, China
| | - Hao Chen
- School of Ophthalmology & Optometry, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
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35
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An Y, Li R, Zhang F, He P. Magneto-Mediated Electrochemical Sensor for Simultaneous Analysis of Breast Cancer Exosomal Proteins. Anal Chem 2020; 92:5404-5410. [PMID: 32157871 DOI: 10.1021/acs.analchem.0c00106] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Breast cancer is a heterogeneous disease, and it lacks special tumor markers. Exosomes, new noninvasive biomarkers, with the proteins on the exosome surface show potential for the diagnosis and prognosis of a tumor. However, assessing the variations of exosomal proteins still faces significant challenges. Herein, a magneto-mediated electrochemical sensor based on host-guest recognition has been developed for simultaneous analysis of breast cancer exosomal proteins. Magnetic beads (MB) modified with CD63 aptamer was first employed to capture exosomes. Silica nanoparticles (SiO2 NPs) was modified with MUC1, HER2, EpCAM, and CEA aptamers for specific exosomal proteins identification, respectively, and functionalized with N-(2-((2-aminoethyl)disulfanyl)ethyl) ferrocene carboxamide (FcNHSSNH2) as the signal molecule. The sandwich structure (MB-exosomes-SiO2 NPs probe) was separated by a magnet, and N-(2-mercaptoethyl) ferrocene carboxamide (FcNHSH) was released to the supernatant by the addition of reductants (dithiothreitol, DTT) that break the disulfide bond of FcNHSSNH2. FcNHSH and the graphene oxide-cucurbit [7](GO-CB[7]) modified screen-printed carbon electrode (SPCE) was employed to monitor the oxidation current signals. In this way, four tumor markers on different breast cancer cells (MCF-7, SK-BR-3, MDA-MB-231, and BT474) derived exosomes were sensitively detected. Furthermore, the present assay enabled accurate analysis of exosomes from breast cancer patients, suggesting the potential of exosome analysis in clinic diagnosis.
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Affiliation(s)
- Yu An
- School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Rui Li
- School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Fan Zhang
- School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Pingang He
- School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
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36
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Chen J, Tang J, Meng HM, Liu Z, Wang L, Geng X, Wu Y, Qu L, Li Z. Recognition triggered assembly of split aptamers to initiate a hybridization chain reaction for wash-free and amplified detection of exosomes. Chem Commun (Camb) 2020; 56:9024-9027. [DOI: 10.1039/d0cc02337j] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A novel split aptamer-based system was developed for the amplified detection of exosomes in situ assisted by a target-induced HCR.
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Affiliation(s)
- Juan Chen
- College of Chemistry
- Green Catalysis Center
- Henan Joint International Research Laboratory of Green Construction of Functional Molecules and Their Bioanalytical Applications
- Zhengzhou University
- Zhengzhou 450001
| | - Jinlu Tang
- School of Basic Medical Sciences
- Zhengzhou University
- Zhengzhou 450001
- P. R. China
| | - Hong-Min Meng
- College of Chemistry
- Green Catalysis Center
- Henan Joint International Research Laboratory of Green Construction of Functional Molecules and Their Bioanalytical Applications
- Zhengzhou University
- Zhengzhou 450001
| | - Zhuo Liu
- College of Chemistry
- Green Catalysis Center
- Henan Joint International Research Laboratory of Green Construction of Functional Molecules and Their Bioanalytical Applications
- Zhengzhou University
- Zhengzhou 450001
| | - Lin Wang
- The Academy of Medical Sciences
- Zhengzhou University
- Zhengzhou 450001
- P. R. China
| | - Xin Geng
- College of Chemistry
- Green Catalysis Center
- Henan Joint International Research Laboratory of Green Construction of Functional Molecules and Their Bioanalytical Applications
- Zhengzhou University
- Zhengzhou 450001
| | - Yanan Wu
- College of Chemistry
- Green Catalysis Center
- Henan Joint International Research Laboratory of Green Construction of Functional Molecules and Their Bioanalytical Applications
- Zhengzhou University
- Zhengzhou 450001
| | - Lingbo Qu
- College of Chemistry
- Green Catalysis Center
- Henan Joint International Research Laboratory of Green Construction of Functional Molecules and Their Bioanalytical Applications
- Zhengzhou University
- Zhengzhou 450001
| | - Zhaohui Li
- College of Chemistry
- Green Catalysis Center
- Henan Joint International Research Laboratory of Green Construction of Functional Molecules and Their Bioanalytical Applications
- Zhengzhou University
- Zhengzhou 450001
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