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Liu YK, Wu X, Hadisurya M, Li L, Kaimakliotis H, Iliuk A, Tao WA. One-Pot Analytical Pipeline for Efficient and Sensitive Proteomic Analysis of Extracellular Vesicles. J Proteome Res 2023; 22:3301-3310. [PMID: 37702715 PMCID: PMC10897859 DOI: 10.1021/acs.jproteome.3c00361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/14/2023]
Abstract
Extracellular vesicle (EV) proteomics emerges as an effective tool for discovering potential biomarkers for disease diagnosis, monitoring, and therapeutics. However, the current workflow of mass spectrometry-based EV proteome analysis is not fully compatible in a clinical setting due to inefficient EV isolation methods and a tedious sample preparation process. To streamline and improve the efficiency of EV proteome analysis, here we introduce a one-pot analytical pipeline integrating a robust EV isolation approach, EV total recovery and purification (EVtrap), with in situ protein sample preparation, to detect urinary EV proteome. By incorporating solvent-driven protein capture and fast on-bead digestion, the one-pot pipeline enabled the whole EV proteome analysis to be completed within one day. In comparison with the existing workflow, the one-pot pipeline was able to obtain better peptide yield and identify the equivalent number of unique EV proteins from 1 mL of urine. Finally, we applied the one-pot pipeline to profile proteomes in urinary EVs of bladder cancer patients. A total of 2774 unique proteins were identified in 53 urine samples using a 15 min gradient library-free data-independent acquisition method. Taken altogether, our novel one-pot analytical pipeline demonstrated its potential for routine and robust EV proteomics in biomedical applications.
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Affiliation(s)
- Yi-Kai Liu
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Xiaofeng Wu
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Marco Hadisurya
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Li Li
- Tymora Analytical Operations, West Lafayette, Indiana 47906, United States
| | - Hristos Kaimakliotis
- Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
| | - Anton Iliuk
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, United States
- Tymora Analytical Operations, West Lafayette, Indiana 47906, United States
| | - W Andy Tao
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, United States
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
- Tymora Analytical Operations, West Lafayette, Indiana 47906, United States
- Purdue Institute for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
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Ke ZB, Lin XD, Chen YH, Lin YZ, Chen SH, Chen SM, Chen Y, Wei Y, Zheng QS, Xue XY, Li XD, Xu N. Role of 18F-FDG-PET/CT in Combination With Neutrophil-Lymphocyte Ratio in the Diagnosis of Upper Urinary Tract Lesion: Can We Accurately Predict Malignant Tumor? Front Oncol 2021; 11:615881. [PMID: 34631509 PMCID: PMC8493284 DOI: 10.3389/fonc.2021.615881] [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: 10/10/2020] [Accepted: 08/16/2021] [Indexed: 11/17/2022] Open
Abstract
Objective To explore whether preoperative 18Fluorine-Fluorodeoxyglucose-positron emission tomography/computed tomography (18F-FDG-PET/CT) in combination with neutrophil–lymphocyte ratio (NLR) could accurately predict malignant lesions of upper urinary tract (UUT). Methods and Materials The clinicopathologic data of a total of 252 patients with UUT lesions receiving surgical treatment at our center from January 2012 to November 2019 were retrospectively analyzed. All patients performed routine preoperative hematological examination, urine cytology, computed tomography urography (CTU), and 18F-FDG-PET/CT. Clinicopathologic data between 179 cases with malignancy (Group 1) and 73 cases with benign lesions (Group 2) were compared. Multivariate logistic regression analysis was used to explore the independent predictors of malignant UUT lesions. Receiver operating characteristic (ROC) curve was used to evaluate the predictive ability. Results Among all patients, univariate analysis showed that NLR, hydronephrosis, CTU indicating malignancy, and PET/CT indicating malignancy were significantly associated with malignant UUT lesions; multivariate analysis revealed that NLR, CTU indicating malignancy, and PET/CT indicating malignancy were independent predictors of malignant UUT lesions; the area under ROC curve (AUC) of NLR, CTU, PET/CT, combining CTU and NLR, combining PET/CT and NLR, and combining PET/CT and CTU were 0.735, 0.788, 0.857, 0.863, 0.913, and 0.919, respectively, for postoperative pathological malignancy. Among 68 patients undergoing ureteroscopy biopsy, univariate analysis suggested that NLR, positive urine exfoliation cytology, CTU indicating malignancy, and PET/CT indicating malignancy were significantly associated with malignant UUT lesions; multivariate analysis demonstrated that positive urine cytology, PET/CT indicating malignancy, and NLR were independent predictors of malignant UUT lesions; the AUC of NLR, ureteroscopy biopsy, and combining PET/CT and NLR were 0.768, 0.853, and 0.839, respectively, for postoperative pathological malignancy. Conclusions Combining preoperative NLR and PET/CT performed well in differentiating benign from malignant UUT lesions, which could not be identified by traditional imaging or urine cytology. Combining preoperative NLR and PET/CT could be used to reduce unnecessary ureteroscopy biopsy, which might result in tumor cell dissemination and risk of associated complications.
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Affiliation(s)
- Zhi-Bin Ke
- Department of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Xiao-Dan Lin
- Department of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Ye-Hui Chen
- Department of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Yun-Zhi Lin
- Department of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Shao-Hao Chen
- Department of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Shao-Ming Chen
- Department of Nuclear Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Yu Chen
- Cancer Bio-Immunotherapy Center, Fujian Medical University Cancer Hospital and Fujian Cancer Hospital, Fuzhou, China.,Department of Medical Oncology, Fujian Medical University Cancer Hospital and Fujian Cancer Hospital, Fuzhou, China
| | - Yong Wei
- Department of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Qing-Shui Zheng
- Department of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Xue-Yi Xue
- Department of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Xiao-Dong Li
- Department of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Ning Xu
- Department of Urology, Urology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
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Xu QH, Yuan Q, Zhang YQ, Li B, Min YL, Ge QM, Liang RB, Shao Y. Ocular Metastasis in Elderly Male Bladder Cancer Patients: Potential Risk Factors. Am J Mens Health 2021; 14:1557988320908998. [PMID: 32146866 PMCID: PMC7065287 DOI: 10.1177/1557988320908998] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Bladder cancer is a common type of tumor among elderly male population; it causes intraocular metastasis (IOM). The study investigated the differences between elderly male bladder cancer patients with and without IOM, and identified risk factors for IOM. In this study, 749 elderly male patients (aged ≥50 years) with bladder cancer were included from November 2003 to December 2016. Differences between the IOM and non-IOM (NIOM) groups were evaluated by chi-square test and Student’s t-test. The binary logistic regression analysis calculates the risk factors. Receiver operating characteristic (ROC) curve analysis was used to assess the diagnostic value of IOM in elderly male patients with bladder cancer. The incidence of IOM in patients with bladder cancer was 1.7%. No significant differences were detected in age and histopathology between the IOM and NIOM groups. According to the study, the IOM group had higher ALP and Cyfra21-1. Binary logistic regression indicated that ALP and Cyfra21-1 were risk factors for IOM in elderly male bladder cancer patients (p < .05). ROC curve analysis revealed area under the curve values for ALP and Cyfra21-1 of 0.913 and 0.814, using cutoff values of 9.65 and 83.5 U/L, respectively. The sensitivity and specificity values for ALP were 61.5% and 95.8%, respectively, while those for Cyfra21-1 were 84.6% and 73.3%. The investigation indicates that ALP and Cyfra21-1 are risk factors for IOM in elderly male patients with bladder cancer and ALP is more reliable at distinguishing IOM from NIOM in elderly male patients with bladder cancer.
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Affiliation(s)
- Qian-Hui Xu
- Department of Ophthalmology, The First Affiliated Hospital of Nanchang University, Jiangxi Province Ocular Disease Clinical Research Center, Nanchang, Jiangxi, People's Republic of China
| | - Qing Yuan
- Department of Ophthalmology, The First Affiliated Hospital of Nanchang University, Jiangxi Province Ocular Disease Clinical Research Center, Nanchang, Jiangxi, People's Republic of China
| | - Yu-Qing Zhang
- Department of Ophthalmology, The First Affiliated Hospital of Nanchang University, Jiangxi Province Ocular Disease Clinical Research Center, Nanchang, Jiangxi, People's Republic of China
| | - Biao Li
- Department of Ophthalmology, The First Affiliated Hospital of Nanchang University, Jiangxi Province Clinical Ophthalmology Institute, Nanchang, Jiangxi, People's Republic of China
| | - You-Lan Min
- Department of Ophthalmology, The First Affiliated Hospital of Nanchang University, Jiangxi Province Clinical Ophthalmology Institute, Nanchang, Jiangxi, People's Republic of China
| | - Qian-Min Ge
- Department of Ophthalmology, The First Affiliated Hospital of Nanchang University, Jiangxi Province Clinical Ophthalmology Institute, Nanchang, Jiangxi, People's Republic of China
| | - Rong-Bin Liang
- Department of Ophthalmology, The First Affiliated Hospital of Nanchang University, Jiangxi Province Clinical Ophthalmology Institute, Nanchang, Jiangxi, People's Republic of China
| | - Yi Shao
- Department of Ophthalmology, The First Affiliated Hospital of Nanchang University, Jiangxi Province Ocular Disease Clinical Research Center, Nanchang, Jiangxi, People's Republic of China
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Xu N, Qu GY, Wu YP, Lin YZ, Chen DN, Li XD, Chen SH, Huang JB, Zheng QS, Xue XY, Wei Y. ARPC4 promotes bladder cancer cell invasion and is associated with lymph node metastasis. J Cell Biochem 2019; 121:231-243. [PMID: 31190401 DOI: 10.1002/jcb.29136] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 05/08/2019] [Accepted: 05/10/2019] [Indexed: 12/30/2022]
Abstract
The significance of actin-related protein 2/3 complex subunit 4 (ARPC4) expression in bladder cancer, and its potential role in the invasion and migration of bladder cancer cells, has yet to be determined. This study was to identify the correlation between ARPC4 and lymph node metastasis, and to determine the role of ARPC4 in the invasive migration of T24 bladder cancer cells. One hundred and ninety-eight bladder cancer tissues and 40 normal bladder and lymph node tissues were examined. Tissue microarrays were constructed and subjected to immunohistochemical stating for ARPC4. Multiple logistic analysis was used to determine risk factors associated with bladder cancer metastasis. ARPC4 expression in T24 bladder cancer cells was suppressed using small interfering RNA and changes in protein levels were determined by Western blot analysis. The proliferation of bladder cancer cells after knocking down of ARPC4 was determined by cell counting kit-8. The effects of ARPC4 knockdown on T24 cell invasion and migration was determined using transwell and wound healing assays. Immunofluorescence analysis was performed to examine changes in pseudopodia formation and actin cytoskeleton structure. The expression of ARPC4 was elevated in bladder cancer tissues than normal tissues (84.3% vs 27.5%, P < 0.001). The multivariate logistic analysis demonstrated that the level of ARPC4, as a risk factor, was correlated with lymphatic metastasis (P < 0.05). ARPC4 knockdown attenuated proliferation, migration, invasion, and pseudopodia formation in T24 cells. ARPC4 expression, as a risk factor, is associated with lymphatic metastasis and is upregulated in bladder cancer tissues in comparison with normal tissues. Inhibition of ARPC4 expression significantly attenuates the proliferation, migration, and invasion of bladder cancer cell, possibly due to defects in pseudopodia formation.
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Affiliation(s)
- Ning Xu
- Department of Urology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Gen-Yi Qu
- Department of Urology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China.,Department of Urology, Zhuzhou Central Hospital, Zhuzhou, China
| | - Yu-Peng Wu
- Department of Urology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Yun-Zhi Lin
- Department of Urology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Dong-Ning Chen
- Department of Urology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Xiao-Dong Li
- Department of Urology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Shao-Hao Chen
- Department of Urology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Jin-Bei Huang
- Department of Urology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Qing-Shui Zheng
- Department of Urology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Xue-Yi Xue
- Department of Urology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Yong Wei
- Department of Urology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
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