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Shin D, Kim Y, Park J, Kim Y. High-throughput Proteomics-Guided Biomarker Discovery of Hepatocellular Carcinoma. Biomed J 2024:100752. [PMID: 38901798 DOI: 10.1016/j.bj.2024.100752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Revised: 06/07/2024] [Accepted: 06/12/2024] [Indexed: 06/22/2024] Open
Abstract
Liver cancer stands as the fifth leading cause of cancer-related deaths globally. Hepatocellular carcinoma (HCC) comprises approximately 85%-90% of all primary liver malignancies. However, only 20-30% of HCC patients qualify for curative therapy, primarily due to the absence of reliable tools for early detection and prognosis of HCC. This underscores the critical need for molecular biomarkers for HCC management. Since proteins reflect disease status directly, proteomics has been utilized in biomarker developments for HCC. In particular, proteomics coupled with liquid chromatography-mass spectrometer (LC-MS) methods facilitate the process of discovering biomarker candidates for diagnosis, prognosis, and therapeutic strategies. In this work, we investigated LC-MS-based proteomics methods through recent reference reviews, with a particular focus on sample preparation and LC-MS methods appropriate for the discovery of HCC biomarkers and their clinical applications. We classified proteomics studies of HCC according to sample types, and we examined the coverage of protein biomarker candidates based on LC-MS methods in relation to study scales and goals. Comprehensively, we proposed protein biomarker candidates categorized by sample types and biomarker types for appropriate clinical use. In this review, we summarized recent LC-MS-based proteomics studies on HCC and proposed potential protein biomarkers. Our findings are expected to expand the understanding of HCC pathogenesis and enhance the efficiency of HCC diagnosis and prognosis, thereby contributing to improved patient outcomes.
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Affiliation(s)
- Dongyoon Shin
- Proteomics Research Team, CHA Institute of Future Medicine, Seongnam, Republic of Korea
| | - Yeongshin Kim
- Proteomics Research Team, CHA Institute of Future Medicine, Seongnam, Republic of Korea; Department of Medical Science, School of Medicine, CHA University, Seongnam, Republic of Korea
| | - Junho Park
- Proteomics Research Team, CHA Institute of Future Medicine, Seongnam, Republic of Korea; Department of Pharmacology, School of Medicine, CHA University, Seongnam, Republic of Korea.
| | - Youngsoo Kim
- Proteomics Research Team, CHA Institute of Future Medicine, Seongnam, Republic of Korea; Department of Medical Science, School of Medicine, CHA University, Seongnam, Republic of Korea.
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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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Molika P, Leetanaporn K, Rungkamoltip P, Roytrakul S, Hanprasertpong J, Navakanitworakul R. Proteomic analysis of small extracellular vesicles unique to cervical cancer. Transl Cancer Res 2023; 12:3113-3128. [PMID: 38130315 PMCID: PMC10731333 DOI: 10.21037/tcr-23-517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 09/22/2023] [Indexed: 12/23/2023]
Abstract
Background Cervical cancer (CC) is the fourth most common cancer in females worldwide. Existing biomarkers for CC, such as squamous cell carcinoma antigens, show low specificity. Hence, a novel biomarker for the diagnosis of CC is required. Through proteomic analysis, this study aimed to distinguish between the small extracellular vesicle (sEV) protein profiles of healthy controls (HC) and CC sera and to identify potential sEV proteins that can serve as biomarkers for CC diagnosis. Methods The number and size distribution of sEVs in HC and CC sera were measured using nanoparticle tracking analysis. Differential ultracentrifugation combined with size-exclusion chromatography was used to isolate and purify sEVs. Liquid chromatography-tandem mass spectrometry was used to identify and compare the protein profiles between patients with CC and HC. Differentially expressed extracellular vesicle (EV) proteins were validated using The Cancer Genome Atlas database. Results The EV particle concentration in patients with CC was marginally higher than that in HC. Proteomic and functional protein analyses revealed a difference in the EV protein profiles between HC and CC and identified proteins that can serve as biomarkers for CC. Conclusions This study provides insights into the potential of sEVs as less invasive biomarkers for CC diagnosis. Validation with a well-designed cohort should be performed to determine the clinical diagnostic value of specific protein markers for CC.
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Affiliation(s)
- Piyatida Molika
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand
| | - Kittinun Leetanaporn
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand
| | - Phetploy Rungkamoltip
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand
| | - Sittiruk Roytrakul
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Jitti Hanprasertpong
- Department of Research and Medical Innovation, Faculty of Medicine Vajira Hospital, Navamindradhiraj University, Bangkok, Thailand
| | - Raphatphorn Navakanitworakul
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand
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Wu Z, Yu X, Zhang S, He Y, Guo W. Novel roles of PIWI proteins and PIWI-interacting RNAs in human health and diseases. Cell Commun Signal 2023; 21:343. [PMID: 38031146 PMCID: PMC10685540 DOI: 10.1186/s12964-023-01368-x] [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: 08/18/2023] [Accepted: 10/26/2023] [Indexed: 12/01/2023] Open
Abstract
Non-coding RNA has aroused great research interest recently, they play a wide range of biological functions, such as regulating cell cycle, cell proliferation, and intracellular substance metabolism. Piwi-interacting RNAs (piRNAs) are emerging small non-coding RNAs that are 24-31 nucleotides in length. Previous studies on piRNAs were mainly limited to evaluating the binding to the PIWI protein family to play the biological role. However, recent studies have shed more lights on piRNA functions; aberrant piRNAs play unique roles in many human diseases, including diverse lethal cancers. Therefore, understanding the mechanism of piRNAs expression and the specific functional roles of piRNAs in human diseases is crucial for developing its clinical applications. Presently, research on piRNAs mainly focuses on their cancer-specific functions but lacks investigation of their expressions and epigenetic modifications. This review discusses piRNA's biogenesis and functional roles and the recent progress of functions of piRNA/PIWI protein complexes in human diseases. Video Abstract.
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Affiliation(s)
- Zeyu Wu
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, 450052, China
- Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, 450052, China
| | - Xiao Yu
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, 450052, China
- Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, 450052, China
| | - Shuijun Zhang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, 450052, China
- Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, 450052, China
| | - Yuting He
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
- Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
- Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, 450052, China.
- Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, 450052, China.
| | - Wenzhi Guo
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
- Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
- Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan Universities, Zhengzhou, 450052, China.
- Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, 450052, China.
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Wong SWK, Tey SK, Mao X, Fung HL, Xiao Z, Wong DKH, Mak L, Yuen M, Ng IO, Yun JP, Gao Y, Yam JWP. Small Extracellular Vesicle-Derived vWF Induces a Positive Feedback Loop between Tumor and Endothelial Cells to Promote Angiogenesis and Metastasis in Hepatocellular Carcinoma. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2302677. [PMID: 37387563 PMCID: PMC10502836 DOI: 10.1002/advs.202302677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 06/07/2023] [Indexed: 07/01/2023]
Abstract
Hepatocellular carcinoma (HCC) is a hypervascular malignancy by which its growth and dissemination are largely driven by the modulation of tumor-derived small extracellular vesicles (sEVs). Proteomic profiling of circulating sEVs of control individuals and HCC patients identifies von Willibrand factor (vWF) to be upregulated progressively along HCC stages. Elevated sEV-vWF levels are found in a larger cohort of HCC-sEV samples and metastatic HCC cell lines compared to their respective normal counterparts. Circulating sEVs of late-stage HCC patients markedly augment angiogenesis, tumor-endothelial adhesion, pulmonary vascular leakiness, and metastasis, which are significantly compromised by anti-vWF antibody. The role of vWF is further corroborated by the enhanced promoting effect of sEVs collected from vWF-overexpressing cells. sEV-vWF modulates endothelial cells through an elevated level of vascular endothelial growth factor A (VEGF-A) and fibroblast growth factor 2 (FGF2). Mechanistically, secreted FGF2 elicits a positive feedback response in HCC via the FGFR4/ERK1 signaling pathway. The co-administration of anti-vWF antibody or FGFR inhibitor significantly improves the treatment outcome of sorafenib in a patient-derived xenograft mouse model. This study reveals mutual stimulation between HCC and endothelial cells by tumor-derived sEVs and endothelial angiogenic factors, facilitating angiogenesis and metastasis. It also provides insights into a new therapeutic strategy involving blocking tumor-endothelial intercellular communication.
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Affiliation(s)
- Samuel Wan Ki Wong
- Department of PathologySchool of Clinical MedicineLi Ka Shing Faculty of MedicineThe University of Hong KongHong Kong
| | - Sze Keong Tey
- Department of PathologySchool of Clinical MedicineLi Ka Shing Faculty of MedicineThe University of Hong KongHong Kong
- Department of SurgerySchool of Clinical MedicineLi Ka Shing Faculty of MedicineThe University of Hong KongHong Kong
| | - Xiaowen Mao
- Department of PathologySchool of Clinical MedicineLi Ka Shing Faculty of MedicineThe University of Hong KongHong Kong
- State Key Laboratory of Liver Research, The University of Hong KongHong Kong
| | - Hiu Ling Fung
- Department of PathologySchool of Clinical MedicineLi Ka Shing Faculty of MedicineThe University of Hong KongHong Kong
| | - Zhi‐Jie Xiao
- Research CentreThe Seventh Affiliated HospitalSun Yat‐sen University518107ShenzhenP. R. China
| | - Danny Ka Ho Wong
- Department of MedicineSchool of Clinical MedicineLi Ka Shing Faculty of MedicineThe University of Hong KongHong Kong
| | - Lung‐Yi Mak
- Department of MedicineSchool of Clinical MedicineLi Ka Shing Faculty of MedicineThe University of Hong KongHong Kong
| | - Man‐Fung Yuen
- Department of MedicineSchool of Clinical MedicineLi Ka Shing Faculty of MedicineThe University of Hong KongHong Kong
| | - Irene Oi‐Lin Ng
- State Key Laboratory of Liver Research, The University of Hong KongHong Kong
| | - Jing Ping Yun
- Department of PathologySun Yat‐sen University Cancer CenterGuangzhouGuangdong510060P. R. China
| | - Yi Gao
- Department of Hepatobiliary Surgery IIZhuJiang HospitalSouthern Medical UniversityGuangzhouGuangdong510280P. R. China
| | - Judy Wai Ping Yam
- Department of PathologySchool of Clinical MedicineLi Ka Shing Faculty of MedicineThe University of Hong KongHong Kong
- State Key Laboratory of Liver Research, The University of Hong KongHong Kong
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Lu X, Li Y, Li Y, Zhang X, Shi J, Feng H, Gao Y, Yu Z. Advances of multi-omics applications in hepatic precancerous lesions and hepatocellular carcinoma: The role of extracellular vesicles. Front Mol Biosci 2023; 10:1114594. [PMID: 37006626 PMCID: PMC10060991 DOI: 10.3389/fmolb.2023.1114594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 03/06/2023] [Indexed: 03/18/2023] Open
Abstract
Due to the lack of distinct early symptoms and specific biomarkers, most patients with hepatocellular carcinoma (HCC) are usually diagnosed at advanced stages, rendering the treatment ineffective and useless. Therefore, recognition of the malady at precancerous lesions and early stages is particularly important for improving patient outcomes. The interest in extracellular vesicles (EVs) has been growing in recent years with the accumulating knowledge of their multiple cargoes and related multipotent roles in the modulation of immune response and tumor progression. By virtue of the rapid advancement of high-throughput techniques, multiple omics, including genomics/transcriptomics, proteomics, and metabolomics/lipidomics, have been widely integrated to analyze the role of EVs. Comprehensive analysis of multi-omics data will provide useful insights for discovery of new biomarkers and identification of therapeutic targets. Here, we review the attainment of multi-omics analysis to the finding of the potential role of EVs in early diagnosis and the immunotherapy in HCC.
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Affiliation(s)
- Xiaona Lu
- Department of Liver Disease, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yuyao Li
- Department of Liver Disease, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yue Li
- Department of Liver Disease, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xuemei Zhang
- Department of Liver Disease, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Jia Shi
- Department of Liver Disease, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Hai Feng
- Institute of Infectious Disease, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
- *Correspondence: Hai Feng, ; Yueqiu Gao, ; Zhuo Yu,
| | - Yueqiu Gao
- Department of Liver Disease, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Institute of Infectious Disease, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
- *Correspondence: Hai Feng, ; Yueqiu Gao, ; Zhuo Yu,
| | - Zhuo Yu
- Department of Liver Disease, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
- *Correspondence: Hai Feng, ; Yueqiu Gao, ; Zhuo Yu,
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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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Li D, Jia S, Wang S, Hu L. Glycoproteomic Analysis of Urinary Extracellular Vesicles for Biomarkers of Hepatocellular Carcinoma. Molecules 2023; 28:molecules28031293. [PMID: 36770959 PMCID: PMC9919939 DOI: 10.3390/molecules28031293] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 01/21/2023] [Accepted: 01/24/2023] [Indexed: 02/03/2023] Open
Abstract
Hepatocellular carcinoma (HCC) accounts for the most common form of primary liver cancer cases and constitutes a major health problem worldwide. The diagnosis of HCC is still challenging due to the low sensitivity and specificity of the serum α-fetoprotein (AFP) diagnostic method. Extracellular vesicles (EVs) are heterogeneous populations of phospholipid bilayer-enclosed vesicles that can be found in many biological fluids, and have great potential as circulating biomarkers for biomarker discovery and disease diagnosis. Protein glycosylation plays crucial roles in many biological processes and aberrant glycosylation is a hallmark of cancer. Herein, we performed a comprehensive glycoproteomic profiling of urinary EVs at the intact N-glycopeptide level to screen potential biomarkers for the diagnosis of HCC. With the control of the spectrum-level false discovery rate ≤1%, 756 intact N-glycopeptides with 154 N-glycosites, 158 peptide backbones, and 107 N-glycoproteins were identified. Out of 756 intact N-glycopeptides, 344 differentially expressed intact N-glycopeptides (DEGPs) were identified, corresponding to 308 upregulated and 36 downregulated N-glycopeptides, respectively. Compared to normal control (NC), the glycoproteins LG3BP, PIGR and KNG1 are upregulated in HCC-derived EVs, while ASPP2 is downregulated. The findings demonstrated that specific site-specific glycoforms in these glycoproteins from urinary EVs could be potential and efficient non-invasive candidate biomarkers for HCC diagnosis.
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Affiliation(s)
- Dejun Li
- Center for Supramolecular Chemical Biology, School of Life Sciences, Jilin University, Changchun 130012, China
- Prenatal Diagnosis Center, Reproductive Medicine Center, The First Hospital of Jilin University, Changchun 130021, China
| | - Shengnan Jia
- Department of Hepatopancreatobiliary Medicine, The Second Hospital, Jilin University, Changchun 130041, China
- Correspondence: (S.J.); (L.H.)
| | - Shuyue Wang
- Center for Supramolecular Chemical Biology, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Lianghai Hu
- Center for Supramolecular Chemical Biology, School of Life Sciences, Jilin University, Changchun 130012, China
- Correspondence: (S.J.); (L.H.)
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Choi H, Ju S, Kang K, Seo MH, Kim JM, Miyoshi E, Yeo MK, Park SY. Terminal fucosylation of haptoglobin in cancer-derived exosomes during cholangiocarcinoma progression. Front Oncol 2023; 13:1183442. [PMID: 37168374 PMCID: PMC10165115 DOI: 10.3389/fonc.2023.1183442] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 04/10/2023] [Indexed: 05/13/2023] Open
Abstract
Background Cholangiocarcinoma (CCA) is a silent tumor with a high mortality rate due to the difficulty of early diagnosis and prediction of recurrence even after timely surgery. Serologic cancer biomarkers have been used in clinical practice, but their low specificity and sensitivity have been problematic. In this study, we aimed to identify CCA-specific glycan epitopes that can be used for diagnosis and to elucidate the mechanisms by which glycosylation is altered with tumor progression. Methods The serum of patients with various cancers was fractioned into membrane-bound and soluble components using serial ultracentrifugation. Lectin blotting was conducted to evaluate glycosylation. Proteins having altered glycosylation were identified using proteomic analysis and further confirmed using immunoblotting analysis. We performed HPLC, gene analysis, real-time cargo tracking, and immunohistochemistry to determine the origin of CCA glycosylation and its underlying mechanisms. Extracellular vesicles (EV) were isolated from the sera of 62 patients with CCA at different clinical stages and inflammatory conditions and used for glycan analysis to assess their clinical significance. Results The results reveal that glycosylation patterns between soluble and membrane-bound fractions differ significantly even when obtained from the same donor. Notably, glycans with α1-3/4 fucose and β1-6GlcNAc branched structures increase specifically in membrane-bound fractions of CCA. Mechanically, it is primarily due to β-haptoglobin (β-Hp) originating from CCA expressing fucosyltransferase-3/4 (FUT 3/4) and N-acetylglucosaminyltransferase-V (MGAT5). Newly synthesized β-Hp is loaded into EVs in early endosomes via a KFERQ-like motif and then secreted from CCA cells to induce tumor progression. In contrast, β-Hp expressed by hepatocytes is secreted in a soluble form that does not affect CCA progression. Moreover, evaluation of EV glycosylation in CCA patients shows that fucosylation level of EV-Hp gradually increases with tumor progression and decreases markedly when the tumors are eliminated by surgery. Conclusion This study suggests that terminal fucosylation of Hp in cancer-derived exosomes can be a novel glycan marker for diagnosis and prognosis of CCA. These findings highlight the potential of glycan analysis in different fractions of serum for biomarker discover for other diseases. Further research is needed to understand the role of fucosylated EVs on CCA progression.
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Affiliation(s)
- Hyewon Choi
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, Republic of Korea
| | - Sungeun Ju
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, Republic of Korea
| | - Keunsoo Kang
- Department of Microbiology, Dankook University, Cheonan, Chungnam, Republic of Korea
| | - Moon-Hyeong Seo
- Natural Product Research Center, Korea Institute of Science and Technology, Gangneung, Republic of Korea
| | - Jin-Man Kim
- Department of Pathology, Chungnam National University School of Medicine, Daejeon, Republic of Korea
| | - Eiji Miyoshi
- Department of Molecular Biochemistry and Clinical Investigation, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Min-Kyung Yeo
- Department of Pathology, Chungnam National University School of Medicine, Daejeon, Republic of Korea
- *Correspondence: Min-Kyung Yeo, ; Seung-Yeol Park,
| | - Seung-Yeol Park
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, Republic of Korea
- *Correspondence: Min-Kyung Yeo, ; Seung-Yeol Park,
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10
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Exosome-Based Theranostics for Liver Diseases. DISEASE MARKERS 2022; 2022:7888906. [DOI: 10.1155/2022/7888906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 08/23/2022] [Accepted: 09/28/2022] [Indexed: 11/06/2022]
Abstract
Exosomes are small extracellular vesicles that can be secreted by any type of cell, released into almost all biological fluids, and extracted from anybody fluid such as blood, urine, saliva, and amniotic fluid. The theranostic role of exosome in liver diseases has been widely studied in recent years. In this review, we briefly introduce the biological characteristics of exosomes and then focus on the theranostics of exosomes in liver diseases, specifically gene delivery associated with liver diseases.
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11
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Shen H, Bai X, Liu J, Liu P, Zhang T. Screening potential biomarkers of cholangiocarcinoma based on gene chip meta-analysis and small-sample experimental research. Front Oncol 2022; 12:1001400. [PMID: 36300097 PMCID: PMC9590411 DOI: 10.3389/fonc.2022.1001400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 09/20/2022] [Indexed: 11/17/2022] Open
Abstract
Cholangiocarcinoma (CCA) is a rare malignant tumor associated with poor prognosis. This study aimed to identify CCA biomarkers by investigating differentially expressed genes (DEGs) between CCA patients and healthy subjects obtained from the Gene Expression Omnibus database. Bioinformatics tools, including the Illumina BaseSpace Correlation Engine (BSCE) and Gene Expression Profiling Interactive Analysis (GEPIA), were used. The initial DEGs from GSE26566, GSE31370, and GSE77984 were analyzed using GEO2R and Venn, and protein–protein interaction networks were constructed using STRING. The BSCE was applied to assess curated CCA studies to select additional DEGs and them DEGs across the 10 biosets, which was supported by findings in the literature. The final 18 DEGs with clinical significance for CCA were further verified using GEPIA. These included CEACAM6, EPCAM, LAMC2, MMP11, KRT7, KRT17, KRT19, SFN, and SOX9, which were upregulated, and ADH1A, ALDOB, AOX1, CTH, FGA, FGB, FGG, GSTA1, and OTC, which were downregulated in CCA patients. Among these 18 genes, 56 groups of genes (two in each group) were significantly related, and none were independently and differentially expressed. The hub genes FGA, OTC, CTH, and MMP11, which were most correlated with the 18 DEGs, were screened using STRING. The significantly low expression of FGA, OTC, and CTH and significantly high expression of MMP11 were verified by immunohistochemical analysis. Overall, four CCA biomarkers were identified that might regulate the occurrence and development of this disease and affect the patient survival rate, and they have the potential to become diagnostic and therapeutic targets for patients with CCA.
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Affiliation(s)
- Hengyan Shen
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, China
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, China
| | - Xinyu Bai
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, China
| | - Jie Liu
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, China
| | - Ping Liu
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, China
- *Correspondence: Tao Zhang, ; Ping Liu,
| | - Tao Zhang
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, China
- *Correspondence: Tao Zhang, ; Ping Liu,
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12
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Xie D, Qian B, Li X. Nucleic acids and proteins carried by exosomes from various sources: Potential role in liver diseases. Front Physiol 2022; 13:957036. [PMID: 36213232 PMCID: PMC9538374 DOI: 10.3389/fphys.2022.957036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 08/17/2022] [Indexed: 12/24/2022] Open
Abstract
Exosomes are extracellular membrane-encapsulated vesicles that are released into the extracellular space or biological fluids by many cell types through exocytosis. As a newly identified form of intercellular signal communication, exosomes mediate various pathological and physiological processes by exchanging various active substances between cells. The incidence and mortality of liver diseases is increasing worldwide. Therefore, we reviewed recent studies evaluating the role of exosomes from various sources in the diagnosis and treatment of liver diseases.
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Affiliation(s)
- Danna Xie
- The First Clinical Medical College of Lanzhou University, Lanzhou, China
| | - Baolin Qian
- Department of Hepatic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xun Li
- The First Clinical Medical College of Lanzhou University, Lanzhou, China
- Department of General Surgery, the First Hospital of Lanzhou University, Lanzhou, China
- Key Laboratory of Biotherapy and Regenerative Medicine of Gansu Province, Lanzhou, China
- Center for Cancer Prevention and Treatment, School of Medicine, Lanzhou University, Lanzhou, China
- Gansu Provincial Institute of Hepatobiliary and Pancreatic Surgery, Lanzhou, China
- *Correspondence: Xun Li,
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13
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DIA-based proteomics analysis of serum-derived exosomal proteins as potential candidate biomarkers for intrahepatic cholestasis in pregnancy. Arch Gynecol Obstet 2022; 308:79-89. [PMID: 35849169 DOI: 10.1007/s00404-022-06703-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 07/03/2022] [Indexed: 11/02/2022]
Abstract
BACKGROUND Data-independent acquisition (DIA) is one of the most powerful and reproducible proteomic technologies for large-scale digital qualitative and quantitative research. The aim of this study was to use proteomic methodologies for the identification of biomarkers that are over or underexpressed in women with intrahepatic cholestasis of pregnancy (ICP) compared with controls and discover a potential biomarker panel for ICP detection. METHODS The participants included 11 ICP patients and 11 healthy pregnant women as controls. The clinical characteristic data and the laboratory biochemical data were collected at the time of recruitment. Then, a data-independent acquisition (DIA)-based proteomics approach was used to identify differentially expressed proteins (DEPs) in serum exosomes between ICP patients and controls. Finally, bioinformatics analysis was used to identify the relevant processes in which these DEPs were involved. RESULTS The proteomics results showed that there were 162 DEPs in serum exosomes between pregnant women with ICP and healthy pregnant women, of which 106 were upregulated and 56 were downregulated in ICP. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the identified proteins were functionally related to specific cell processes including apoptosis, lipid metabolism, immune response and cell proliferation, and metabolic disorders, suggesting that these may be primary causative factors in ICP pathogenesis. Meanwhile, complement and coagulation cascades may be closely related to the development of ICP. Receiver operating characteristic curve (ROC) analysis showed that the area under the curve values of Elongation factor 1-alpha 1, Beta-2-glycoprotein I, Zinc finger protein 238, CP protein and Ficolin-3 were all approximately 0.9, indicating the promising diagnostic value of these proteins. CONCLUSIONS This preliminary work provides a better understanding of the proteomic alterations in the serum exosomes of pregnant women with ICP.
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14
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Thakur A, Parra DC, Motallebnejad P, Brocchi M, Chen HJ. Exosomes: Small vesicles with big roles in cancer, vaccine development, and therapeutics. Bioact Mater 2021; 10:281-294. [PMID: 34901546 PMCID: PMC8636666 DOI: 10.1016/j.bioactmat.2021.08.029] [Citation(s) in RCA: 104] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/23/2021] [Accepted: 08/25/2021] [Indexed: 12/11/2022] Open
Abstract
Cancer is a deadly disease that is globally and consistently one of the leading causes of mortality every year. Despite the availability of chemotherapy, radiotherapy, immunotherapy, and surgery, a cure for cancer has not been attained. Recently, exosomes have gained significant attention due to the therapeutic potential of their various components including proteins, lipids, nucleic acids, miRNAs, and lncRNAs. Exosomes constitute a set of tiny extracellular vesicles with an approximate diameter of 30-100 nm. They are released from different cells and are present in biofluids including blood, cerebrospinal fluid (CSF), and urine. They perform crucial multifaceted functions in the malignant progression of cancer via autocrine, paracrine, and endocrine communications. The ability of exosomes to carry different cargoes including drug and molecular information to recipient cells make them a novel tool for cancer therapeutics. In this review, we discuss the major components of exosomes and their role in cancer progression. We also review important literature about the potential role of exosomes as vaccines and delivery carriers in the context of cancer therapeutics.
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Affiliation(s)
- Abhimanyu Thakur
- Pritzker School of Molecular Engineering, The University of Chicago, United States.,Ben May Department for Cancer Research, The University of Chicago, United States
| | - Diana Carolina Parra
- Tropical Disease Laboratory, Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), São Paulo, Brazil
| | - Pedram Motallebnejad
- Pritzker School of Molecular Engineering, The University of Chicago, United States.,Ben May Department for Cancer Research, The University of Chicago, United States
| | - Marcelo Brocchi
- Tropical Disease Laboratory, Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), São Paulo, Brazil
| | - Huanhuan Joyce Chen
- Pritzker School of Molecular Engineering, The University of Chicago, United States.,Ben May Department for Cancer Research, The University of Chicago, United States
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15
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Xu D, Wu J, Dong L, Luo W, Li L, Tang D, Liu J. Serpinc1 Acts as a Tumor Suppressor in Hepatocellular Carcinoma Through Inducing Apoptosis and Blocking Macrophage Polarization in an Ubiquitin-Proteasome Manner. Front Oncol 2021; 11:738607. [PMID: 34881176 PMCID: PMC8645897 DOI: 10.3389/fonc.2021.738607] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 10/29/2021] [Indexed: 01/02/2023] Open
Abstract
Serpinc1 is a serine protease inhibitor in the coagulation cascade, but its role in tumor biology remains obscure. Here, we report an unexpected role of serpinc1 in suppression of hepatocellular carcinoma (HCC). In HCC patients, the mRNA and protein expression of serpinc1 is upregulated, which is negatively correlated with tumor grade, and has a better prognosis than patients with low serpinc1. In addition, patients with high expression of serpinc1 generally have a better tumor immune microenvironment, accompanied by changes in multiple immune cells and mediators. In particular, tumor-promoting M2 macrophages are negatively correlated with serpinc1 expression and the prognosis of HCC patients. In vitro experiments further show that overexpression of serpinc1 inhibits the growth of HCC cells (HepG2 and SMMC7721) by inducing apoptosis. Accordingly, cell co-culture experiments reveal the direct role of serpinc1-overexpressed HCC cells in inhibiting the formation of M2 macrophages. Subsequent unbiased quantitative proteomic and ubiquitinome analyses identify that multiple poly-ubiquitination of proteins involved in signal pathways (such as autophagy, apoptosis, lactate metabolism, and VEGF signaling) are regulated by serpinc1. Overall, these findings establish a serpinc1-dependent ubiquitin-proteasome system to control apoptosis and antitumor immunity.
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Affiliation(s)
- Dacai Xu
- Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China.,Institute Pasteur of Shanghai, Chinese Academy of Science, Shanghai, China
| | - Jiawen Wu
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
| | - Liang Dong
- Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Wenwen Luo
- Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Lanying Li
- Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Daolin Tang
- Department of Surgery, University of Texas (UT) Southwestern Medical Center, Dallas, TX, United States
| | - Jinbao Liu
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
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16
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Zhu J, Zhang J, Ji X, Tan Z, Lubman DM. Column-based Technology for CD9-HPLC Immunoaffinity Isolation of Serum Extracellular Vesicles. J Proteome Res 2021; 20:4901-4911. [PMID: 34473505 DOI: 10.1021/acs.jproteome.1c00549] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Serum-derived extracellular vesicles (EVs) are a promising source of biomarkers; however, major challenges in EV separation and proteomic profiling remain for isolating EVs from a small amount, that is, on the microliter scale, of human serum while minimizing the contamination of blood proteins and lipoprotein particles coeluting in EV preparations. Herein we have developed a column-based CD9-antibody-immobilized high-performance liquid chromatography immunoaffinity chromatography(CD9-HPLC-IAC) technology for EV isolation from a microliter scale of serum for downstream proteomic analysis. The CD9-HPLC-IAC method achieved EV isolation from 40 μL of serum in 30 min with a yield of 8.0 × 109 EVs, where EVs were further processed with a postcolumn cleaning step using the 50 kDa molecular weight cut-off filter for the buffer exchange, concentration, and reduction of potentially coeluting serum proteins. In total, 482 proteins were identified in EVs by using liquid chromatography tandem mass spectrometry, including the common exosomal markers such as CD63, CD81, CD82, Alix, and TSG101. The statistical analysis of EV protein content showed that the top 10 serum proteins in EVs were significantly decreased by using the CD9-HPLC-IAC method compared with the use of ultracentrifugation (p = 0.001) and size exclusion chromatography (p = 0.009), and apolipoproteins were significantly reduced 4.8-fold compared with the SEC method (p < 0.001). The result demonstrates the potential of the CD9-HPLC-IAC method for the efficient isolation and proteomic characterization of EVs from a microscale volume of serum.
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Affiliation(s)
- Jianhui Zhu
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, Michigan 48109, United States
| | - Jie Zhang
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, Michigan 48109, United States
| | - Xiaohui Ji
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, Michigan 48109, United States.,Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing 400030, China
| | - Zhijing Tan
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, Michigan 48109, United States
| | - David M Lubman
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, Michigan 48109, United States
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