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Zhang H, Zhang GY, Su WC, Chen YT, Liu YF, Wei D, Zhang YX, Tang QY, Liu YX, Wang SZ, Li WC, Wesselius A, Zeegers MP, Zhang ZY, Gu YH, Tao WA, Yu EYW. High Throughput Isolation and Data Independent Acquisition Mass Spectrometry (DIA-MS) of Urinary Extracellular Vesicles to Improve Prostate Cancer Diagnosis. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27238155. [PMID: 36500247 PMCID: PMC9737666 DOI: 10.3390/molecules27238155] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 11/17/2022] [Accepted: 11/19/2022] [Indexed: 11/25/2022]
Abstract
Proteomic profiling of extracellular vesicles (EVs) represents a promising approach for early detection and therapeutic monitoring of diseases such as cancer. The focus of this study was to apply robust EV isolation and subsequent data-independent acquisition mass spectrometry (DIA-MS) for urinary EV proteomics of prostate cancer and prostate inflammation patients. Urinary EVs were isolated by functionalized magnetic beads through chemical affinity on an automatic station, and EV proteins were analyzed by integrating three library-base analyses (Direct-DIA, GPF-DIA, and Fractionated DDA-base DIA) to improve the coverage and quantitation. We assessed the levels of urinary EV-associated proteins based on 40 samples consisting of 20 cases and 20 controls, where 18 EV proteins were identified to be differentiated in prostate cancer outcome, of which three (i.e., SERPINA3, LRG1, and SCGB3A1) were shown to be consistently upregulated. We also observed 6 out of the 18 (33%) EV proteins that had been developed as drug targets, while some of them showed protein-protein interactions. Moreover, the potential mechanistic pathways of 18 significantly different EV proteins were enriched in metabolic, immune, and inflammatory activities. These results showed consistency in an independent cohort with 20 participants. Using a random forest algorithm for classification assessment, including the identified EV proteins, we found that SERPINA3, LRG1, or SCGB3A1 add predictable value in addition to age, prostate size, body mass index (BMI), and prostate-specific antigen (PSA). In summary, the current study demonstrates a translational workflow to identify EV proteins as molecular markers to improve the clinical diagnosis of prostate cancer.
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Affiliation(s)
- Hao Zhang
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, Southeast University, Nanjing 210096, China
- EVLiXiR Biotech, Nanjing 210032, China
| | - Gui-Yuan Zhang
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, Southeast University, Nanjing 210096, China
- EVLiXiR Biotech, Nanjing 210032, China
| | - Wei-Chao Su
- Department of Colorectal Tumor Surgery, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen 361003, China
- Department of Mental Health Research, Xiamen Xianyue Hospital, Xiamen 361012, China
| | - Ya-Ting Chen
- Key Laboratory of Environmental Medicine and Engineering of Ministry of Education, Department of Epidemiology & Biostatistics, School of Public Health, Southeast University, Nanjing 210009, China
| | - Yu-Feng Liu
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, Southeast University, Nanjing 210096, China
- EVLiXiR Biotech, Nanjing 210032, China
- Bell Mountain Molecular MedTech Institute, Nanjing 210032, China
| | - Dong Wei
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, Southeast University, Nanjing 210096, China
- Bell Mountain Molecular MedTech Institute, Nanjing 210032, China
| | - Yan-Xi Zhang
- Key Laboratory of Environmental Medicine and Engineering of Ministry of Education, Department of Epidemiology & Biostatistics, School of Public Health, Southeast University, Nanjing 210009, China
| | - Qiu-Yi Tang
- Medical School of Southeast University, Nanjing 210009, China
| | - Yu-Xiang Liu
- Key Laboratory of Environmental Medicine and Engineering of Ministry of Education, Department of Epidemiology & Biostatistics, School of Public Health, Southeast University, Nanjing 210009, China
| | - Shi-Zhi Wang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China
| | - Wen-Chao Li
- Department of Urology, Affiliated Zhongda Hospital of Southeast University, Nanjing 210009, China
| | - Anke Wesselius
- Department of Epidemiology, CAPHRI Care and Public Health Research Institute, Maastricht University, 6229ER Maastricht, The Netherlands
- School of Nutrition and Translational Research in Metabolism, Maastricht University, 6229ER Maastricht, The Netherlands
| | - Maurice P. Zeegers
- Department of Epidemiology, CAPHRI Care and Public Health Research Institute, Maastricht University, 6229ER Maastricht, The Netherlands
- School of Nutrition and Translational Research in Metabolism, Maastricht University, 6229ER Maastricht, The Netherlands
| | - Zi-Yu Zhang
- Department of Pathology, Jiangxi Maternal & Child Health Hospital, Nanchang 330006, China
| | - Yan-Hong Gu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing 210029, China
| | - W. Andy Tao
- Departments of Chemistry and Biochemistry, Purdue University, West Lafayette, IN 47907, USA
- Correspondence: (W.A.T.); (E.Y.-W.Y.)
| | - Evan Yi-Wen Yu
- Key Laboratory of Environmental Medicine and Engineering of Ministry of Education, Department of Epidemiology & Biostatistics, School of Public Health, Southeast University, Nanjing 210009, China
- Department of Epidemiology, CAPHRI Care and Public Health Research Institute, Maastricht University, 6229ER Maastricht, The Netherlands
- Correspondence: (W.A.T.); (E.Y.-W.Y.)
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Ciereszko A, Dietrich MA, Słowińska M, Nynca J, Ciborowski M, Kaczmarek MM, Myszczyński K, Kiśluk J, Majewska A, Michalska-Falkowska A, Kodzik N, Reszeć J, Sierko E, Nikliński J. Application of two-dimensional difference gel electrophoresis to identify protein changes between center, margin, and adjacent non-tumor tissues obtained from non-small-cell lung cancer with adenocarcinoma or squamous cell carcinoma subtype. PLoS One 2022; 17:e0268073. [PMID: 35512017 PMCID: PMC9071164 DOI: 10.1371/journal.pone.0268073] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 04/21/2022] [Indexed: 12/12/2022] Open
Abstract
Lung cancer is responsible for the most cancer-related mortality worldwide and the mechanism of its development is poorly understood. Proteomics has become a powerful tool offering vital knowledge related to cancer development. Using a two-dimensional difference gel electrophoresis (2D-DIGE) approach, we sought to compare tissue samples from non-small-cell lung cancer (NSCLC) patients taken from the tumor center and tumor margin. Two subtypes of NSCLC, adenocarcinoma (ADC) and squamous cell carcinoma (SCC) were compared. Data are available via ProteomeXchange with identifier PXD032736 and PXD032962 for ADC and SCC, respectively. For ADC proteins, 26 significant canonical pathways were identified, including Rho signaling pathways, a semaphorin neuronal repulsive signaling pathway, and epithelial adherens junction signaling. For SCC proteins, nine significant canonical pathways were identified, including hypoxia-inducible factor-1α signaling, thyroid hormone biosynthesis, and phagosome maturation. Proteins differentiating the tumor center and tumor margin were linked to cancer invasion and progression, including cell migration, adhesion and invasion, cytoskeletal structure, protein folding, anaerobic metabolism, tumor angiogenesis, EMC transition, epithelial adherens junctions, and inflammatory responses. In conclusion, we identified several proteins that are important for the better characterization of tumor development and molecular specificity of both lung cancer subtypes. We also identified proteins that may be important as biomarkers and/or targets for anticancer therapy.
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Affiliation(s)
- Andrzej Ciereszko
- Department of Gametes and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
- * E-mail:
| | - Mariola A. Dietrich
- Department of Gametes and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
| | - Mariola Słowińska
- Department of Gametes and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
| | - Joanna Nynca
- Department of Gametes and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
| | - Michał Ciborowski
- Metabolomics Laboratory, Clinical Research Centre, Medical University of Bialystok, Bialystok, Poland
| | - Monika M. Kaczmarek
- Molecular Biology Laboratory, Institute of Animal Reproduction and Food Research Polish Academy of Sciences, Olsztyn, Poland
| | - Kamil Myszczyński
- Molecular Biology Laboratory, Institute of Animal Reproduction and Food Research Polish Academy of Sciences, Olsztyn, Poland
| | - Joanna Kiśluk
- Department of Clinical Molecular Biology, Medical University of Bialystok, Bialystok, Poland
| | - Anna Majewska
- Department of Gametes and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
| | | | - Natalia Kodzik
- Department of Gametes and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
| | - Joanna Reszeć
- Department of Medical Pathomorphology, Medical University of Bialystok, Bialystok, Poland
| | - Ewa Sierko
- Department of Oncology, Medical University of Bialystok, Bialystok, Poland
| | - Jacek Nikliński
- Department of Clinical Molecular Biology, Medical University of Bialystok, Bialystok, Poland
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Jiang C, Li X, Sun B, Zhang N, Li J, Yue S, Hu X. Extracellular vesicles promotes liver metastasis of lung cancer by ALAHM increasing hepatocellular secretion of HGF. iScience 2022; 25:103984. [PMID: 35281743 PMCID: PMC8914534 DOI: 10.1016/j.isci.2022.103984] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/09/2022] [Accepted: 02/21/2022] [Indexed: 11/18/2022] Open
Affiliation(s)
- Chunyang Jiang
- Department of Thoracic Surgery, Tianjin Union Medical Center, Nankai University, 190 Jieyuan Road, Hongqiao District, Tianjin 300121, Tianjin, China
- Corresponding author
| | - Xu Li
- Department of Thoracic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, Fujian Province, China
| | - Bingsheng Sun
- Department of Thoracic Surgery, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin 300060, Tianjin, China
| | - Na Zhang
- Department of Respiratory Medicine, Tianjin Union Medical Center, Nankai University, 190 Jieyuan Road, Hongqiao District, Tianjin 300121, Tianjin, China
| | - Jing Li
- Department of Respiratory Medicine, Tianjin Union Medical Center, Nankai University, 190 Jieyuan Road, Hongqiao District, Tianjin 300121, Tianjin, China
| | - Shijing Yue
- The State Key Laboratory of Medicinal Chemical Biology, School of Medicine, The State International Science & Technology Cooperation Base of Tumor Immunology and Biological Vaccines, Nankai University, 94 Weijin Road, Nankai District, Tianjin 300071, Tianjin, China
- Corresponding author
| | - Xiaoli Hu
- Department of Respiratory Medicine, The Second People’|'s Hospital of Linhai City, 198 Dubei Road, Linhai 317016, Zhejiang Province, China
- Corresponding author
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Garafutdinov RR, Sakhabutdinova AR, Gilvanov AR, Chemeris AV. Rolling Circle Amplification as a Universal Method for the Analysis of a Wide Range of Biological Targets. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2021; 47:1172-1189. [PMID: 34931113 PMCID: PMC8675116 DOI: 10.1134/s1068162021060078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/14/2021] [Accepted: 04/16/2021] [Indexed: 11/23/2022]
Abstract
Detection and quantification of biotargets are important analytical tasks, which are solved using a wide range of various methods. In recent years, methods based on the isothermal amplification of nucleic acids (NAs) have been extensively developed. Among them, a special place is occupied by rolling circle amplification (RCA), which is used not only for the detection of a specific NA but also for the analysis of other biomolecules, and is also a versatile platform for the development of highly sensitive methods and convenient diagnostic devices. The present review reveals a number of methodical aspects of RCA-mediated analysis; in particular, the data on its key molecular participants are presented, the methods for increasing the efficiency and productivity of RCA are described, and different variants of reporter systems are briefly characterized. Differences in the techniques of RCA-mediated analysis of biotargets of various types are shown. Some examples of using different RCA variants for the solution of specific diagnostic problems are given.
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Affiliation(s)
- R. R. Garafutdinov
- Institute of Biochemistry and Genetics, Ufa Federal Research Center, Russian Academy of Sciences, 450054 Ufa, Russia
| | - A. R. Sakhabutdinova
- Institute of Biochemistry and Genetics, Ufa Federal Research Center, Russian Academy of Sciences, 450054 Ufa, Russia
| | - A. R. Gilvanov
- Institute of Biochemistry and Genetics, Ufa Federal Research Center, Russian Academy of Sciences, 450054 Ufa, Russia
| | - A. V. Chemeris
- Institute of Biochemistry and Genetics, Ufa Federal Research Center, Russian Academy of Sciences, 450054 Ufa, Russia
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Zhao X, Luo C, Mei Q, Zhang H, Zhang W, Su D, Fu W, Luo Y. Aptamer-Cholesterol-Mediated Proximity Ligation Assay for Accurate Identification of Exosomes. Anal Chem 2020; 92:5411-5418. [PMID: 32207293 DOI: 10.1021/acs.analchem.0c00141] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Accurate identification of exosomes plays an essential role in facilitating disease diagnosis and therapies. Herein, we proposed an Aptamer-cholesterol-mediated Proximity Ligation Assay (AcmPLA) for accurate identification of exosomes in a dual-probe strategy, one aptamer probe for recognition of exosomal innate surface protein CD63 and another cholesterol probe for biolipid layer targeting. By integrating a proximity ligation of probes bound with exosomal biomarkers for specific recognition and a rolling circle amplification (RCA) strategy for signal amplification, we have successfully developed an exosomes-surface approach that can perform "AND" logic analysis of dual biomarkers, which not only could be used for exosomes quantification, but also for exosomes tracing. Besides RCA-initiated signal amplification, CD9 antibody-labeled magnetic beads were used to capture exosomes for isolation and secondary signal enrichment. Our approach can achieve specific exosomes isolation and accurate identification and thus could be exploited for broad applications in biological science, biomedical engineering, and personalized medicine.
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Affiliation(s)
- Xianxian Zhao
- Department of Clinical Laboratory, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China.,Center for Smart Laboratory and Molecular Medicine, Medical School of Chongqing University, Chongqing, 400044, China
| | - Canjun Luo
- Department of General Surgery, The 906th Hospital of PLA, Ningbo, 325099, China
| | - Qiang Mei
- Department of Clinical Laboratory, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China
| | - Hongmin Zhang
- The First People's Hospital of Chongqing Liang Jiang New Area, Chongqing, 401121, China
| | - Wenqing Zhang
- Department of Clinical Laboratory, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China
| | - Dongwei Su
- Department of General Surgery, Changhai Hospital, The Second Military Medical University, Shanghai, 200433, China
| | - Weiling Fu
- Department of Clinical Laboratory, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China
| | - Yang Luo
- Center for Smart Laboratory and Molecular Medicine, Medical School of Chongqing University, Chongqing, 400044, China.,Nuclear Medicine and Molecular Imaging Key Laboratory of Sichuan Province, Department of Nuclear Medicine, the Affiliated Hospital, Southwest Medical University, Luzhou, Sichuan 646000, China
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