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Zhang H, Deng Y, Liu X, Sun J, Ma L, Ding Y, Zhan Z, Zhang H, Yang Y, Gu Y, Iliuk AB, Yang C, Tao WA. Glass Fiber-Supported Hybrid Monolithic Spin Tip for Enrichment of Phosphopeptides from Urinary Extracellular Vesicles. Anal Chem 2020; 92:14790-14797. [PMID: 33074658 PMCID: PMC8281360 DOI: 10.1021/acs.analchem.0c03557] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Extracellular vesicles (EVs) are attracting increasing interest with their intriguing role in intercellular communications. Protein phosphorylation in EVs is of great importance for understanding intercellular signaling processes. However, the study of EV phosphoproteomics is impeded by their relatively low amount in limited clinical sample volumes, and it is necessary to have a sensitive and efficient enrichment method for EV phosphopeptides. Herein, a novel Ti(IV)-functionalized and glass fiber-supported hybrid monolithic spin tip, termed PhosTip, was prepared for enriching phosphopeptides from urinary EVs. Glass fiber as the stationary phase positions the hybrid monolith in a standard pipet tip and prevents the monolith from distortion during experiments. The preparation procedure for the new PhosTip is simple and time-saving. The hybrid monolithic PhosTip provides excellent enrichment efficiency of low-abundance phosphopeptides from cell digests and urinary EVs with minimum contamination and sample loss. Using the PhosTip, we demonstrate that 5373 and 336 unique phosphopeptides were identified from 100 and 1 μg of cell lysates, while 3919 and 217 unique phosphopeptides were successfully identified from 10 and 1 mL of urinary samples, respectively. The PhosTip was finally applied to enrich phosphopeptides in urine EVs from prostate cancer patients and healthy controls and quantify 118 up-regulated proteins with phosphosites in prostate cancer samples. These results demonstrated that the PhosTip could be a simple and convenient tool for enriching phosphopeptides from clinical samples and for broader applications in biomarker discovery.
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Affiliation(s)
- Haiyang Zhang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, No. 2 Sipailou, Nanjing 210009, China
| | - Yuanyuan Deng
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, No. 2 Sipailou, Nanjing 210009, China
| | - Xinyi Liu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, No. 2 Sipailou, Nanjing 210009, China
| | - Jie Sun
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, No. 2 Sipailou, Nanjing 210009, China
| | - Leyao Ma
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, No. 2 Sipailou, Nanjing 210009, China
| | - Yajie Ding
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, No. 2 Sipailou, Nanjing 210009, China
| | - Zhen Zhan
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, No. 2 Sipailou, Nanjing 210009, China
| | - Hao Zhang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, No. 2 Sipailou, Nanjing 210009, China
| | - Yuchen Yang
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, No. 68, Changle Road, Nanjing 210009, China
| | - Yanhong Gu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, No. 68, Changle Road, Nanjing 210009, China
| | - Anton B Iliuk
- Tymora Analytical Operations, West Lafayette, Indiana 47906, United States
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Chenxi Yang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, No. 2 Sipailou, Nanjing 210009, China
| | - W Andy Tao
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, United States
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
- Purdue Center of Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
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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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Wang YT, Shi T, Srivastava S, Kagan J, Liu T, Rodland KD. Proteomic Analysis of Exosomes for Discovery of Protein Biomarkers for Prostate and Bladder Cancer. Cancers (Basel) 2020; 12:cancers12092335. [PMID: 32825017 PMCID: PMC7564640 DOI: 10.3390/cancers12092335] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 08/11/2020] [Accepted: 08/16/2020] [Indexed: 12/15/2022] Open
Abstract
Extracellular vesicles (EVs) are released by nearly all cell types as part of normal cell physiology, transporting biological cargo, including nucleic acids and proteins, across the cell membrane. In pathological states such as cancer, EV-derived cargo may mirror the altered state of the cell of origin. Exosomes are the smaller, 50–150 nanometer-sized EVs released from fusion of multivesicular endosomes with the plasma membrane. Exosomes play important roles in cell-cell communication and participate in multiple cancer processes, including invasion and metastasis. Therefore, proteomic analysis of exosomes is a promising approach to discover potential cancer biomarkers, even though it is still at an early stage. Herein, we critically review the advances in exosome isolation methods and their compatibility with mass spectrometry (MS)-based proteomic analysis, as well as studies of exosomes in pathogenesis and progression of prostate and bladder cancer, two common urologic cancers whose incidence rates continue to rise annually. As urological tumors, both urine and blood samples are feasible for noninvasive or minimally invasive analysis. A better understanding of the biological cargo and functions of exosomes via high-throughput proteomics will help provide new insights into complex alterations in cancer and provide potential therapeutic targets and personalized treatment for patients.
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Affiliation(s)
- Yi-Ting Wang
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA; (Y.-T.W.); (T.S.)
| | - Tujin Shi
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA; (Y.-T.W.); (T.S.)
| | - Sudhir Srivastava
- Cancer Biomarkers Research Group, Division of Cancer Prevention, National Cancer Institute, Bethesda, MD 20892, USA; (S.S.); (J.K.)
| | - Jacob Kagan
- Cancer Biomarkers Research Group, Division of Cancer Prevention, National Cancer Institute, Bethesda, MD 20892, USA; (S.S.); (J.K.)
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA; (Y.-T.W.); (T.S.)
- Correspondence: (T.L.); (K.D.R.)
| | - Karin D. Rodland
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA; (Y.-T.W.); (T.S.)
- Department of Cell, Developmental, and Cancer Biology, Oregon Health and Science University, Portland, OR 97201, USA
- Correspondence: (T.L.); (K.D.R.)
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Iliuk A, Wu X, Li L, Sun J, Hadisurya M, Boris RS, Tao WA. Plasma-Derived Extracellular Vesicle Phosphoproteomics through Chemical Affinity Purification. J Proteome Res 2020; 19:2563-2574. [PMID: 32396726 DOI: 10.1021/acs.jproteome.0c00151] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The invasive nature and the pain caused to patients inhibit the routine use of tissue biopsy-based procedures for cancer diagnosis and surveillance. The analysis of extracellular vesicles (EVs) from biofluids has recently gained significant traction in the liquid biopsy field. EVs offer an essential "snapshot" of their precursor cells in real time and contain an information-rich collection of nucleic acids, proteins, lipids, and so on. The analysis of protein phosphorylation, as a direct marker of cellular signaling and disease progression could be an important stepping stone to successful liquid biopsy applications. Here we introduce a rapid EV isolation method based on chemical affinity called EVtrap (extracellular vesicle total recovery and purification) for the EV phosphoproteomics analysis of human plasma. By incorporating EVtrap with high-performance mass spectrometry (MS), we were able to identify over 16 000 unique peptides representing 2238 unique EV proteins from just 5 μL of plasma sample, including most known EV markers, with substantially higher recovery levels compared with ultracentrifugation. Most importantly, more than 5500 unique phosphopeptides representing almost 1600 phosphoproteins in EVs were identified using only 1 mL of plasma. Finally, we carried out a quantitative EV phosphoproteomics analysis of plasma samples from patients diagnosed with chronic kidney disease or kidney cancer, identifying dozens of phosphoproteins capable of distinguishing disease states from healthy controls. The study demonstrates the potential feasibility of our robust analytical pipeline for cancer signaling monitoring by tracking plasma EV phosphorylation.
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Affiliation(s)
- Anton Iliuk
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, United States.,Tymora Analytical Operations, West Lafayette, Indiana 47906, United States
| | - Xiaofeng Wu
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Li Li
- Tymora Analytical Operations, West Lafayette, Indiana 47906, United States
| | - Jie Sun
- College of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Marco Hadisurya
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Ronald S Boris
- Department of Urology, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
| | - W Andy Tao
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, United States.,Tymora Analytical Operations, West Lafayette, Indiana 47906, United States.,Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States.,College of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.,Purdue Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
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Abstract
Extracellular vesicles (EVs) play an important role in cell-to-cell communication by carrying molecular messages that reflect physiological and pathological conditions of the parent cells. EVs have been identified in all body fluids; and among them, urine stands out as a sample that is easy and inexpensive to obtain and can be collected over time to monitor changes. Various protocols have been established to study urinary extracellular vesicles (UEVs) and they have shown great potential as a biomarker source for clinical applications, not only for urological, but also non-urological diseases. Due to the high variability and low reproducibility of pre-analytical and analytical methods for UEVs, establishing a standardized protocol remains a challenge in the field of diagnosis. Here, we review UEV studies and present the techniques that are most commonly used, those that have been applied as new developments, and those that have the most potential for future applications. The workflow procedures from the sampling step to the qualitative and quantitative analysis steps are summarized along with advantages and disadvantages of the methodologies, in order to give consideration for choosing the most promising and suitable method to analyze human UEVs.
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Affiliation(s)
- Piyawan Paisrisarn
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University
| | - Takao Yasui
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University.,Japan Science and Technology Agency (JST), PRESTO.,Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University
| | - Yoshinobu Baba
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University.,Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University.,Institute of Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology
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Andaluz Aguilar H, Iliuk AB, Chen IH, Tao WA. Sequential phosphoproteomics and N-glycoproteomics of plasma-derived extracellular vesicles. Nat Protoc 2019; 15:161-180. [PMID: 31863077 DOI: 10.1038/s41596-019-0260-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 10/16/2019] [Indexed: 12/22/2022]
Abstract
Extracellular vesicles (EVs) are increasingly being recognized as important vehicles for intercellular communication and as promising sources for biomarker discovery. Because the state of protein post-translational modifications (PTMs) such as phosphorylation and glycosylation can be a key determinant of cellular physiology, comprehensive characterization of protein PTMs in EVs can be particularly valuable for early-stage diagnostics and monitoring of disease status. However, the analysis of PTMs in EVs has been complicated by limited amounts of purified EVs, low-abundance PTM proteins, and interference from proteins and metabolites in biofluids. Recently, we developed an approach to isolate phosphoproteins and glycoproteins in EVs from small volumes of human plasma that enabled us to identify nearly 10,000 unique phosphopeptides and 1,500 unique N-glycopeptides. The approach demonstrated the feasibility of using these data to identify potential markers to differentiate disease from healthy states. Here we present an updated workflow to sequentially isolate phosphopeptides and N-glycopeptides, enabling multiple PTM analyses of the same clinical samples. In this updated workflow, we have improved the reproducibility and efficiency of EV isolation, protein extraction, and phosphopeptide/N-glycopeptide enrichment to achieve sensitive analyses of low-abundance PTMs in EVs isolated from 1 mL of plasma. The modularity of the workflow also allows for the characterization of phospho- or glycopeptides only and enables additional analysis of total proteomes and other PTMs of interest. After blood collection, the protocol takes 2 d, including EV isolation, PTM/peptide enrichment, mass spectrometry analysis, and data quantification.
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Affiliation(s)
| | - Anton B Iliuk
- Tymora Analytical Operations, West Lafayette, IN, USA.,Department of Biochemistry, Purdue University, West Lafayette, IN, USA
| | - I-Hsuan Chen
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
| | - W Andy Tao
- Department of Chemistry, Purdue University, West Lafayette, IN, USA. .,Tymora Analytical Operations, West Lafayette, IN, USA. .,Department of Biochemistry, Purdue University, West Lafayette, IN, USA. .,Purdue Center for Cancer Research, Purdue University, West Lafayette, IN, USA.
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