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Joshi N, Garapati K, Ghose V, Kandasamy RK, Pandey A. Recent progress in mass spectrometry-based urinary proteomics. Clin Proteomics 2024; 21:14. [PMID: 38389064 PMCID: PMC10885485 DOI: 10.1186/s12014-024-09462-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 02/12/2024] [Indexed: 02/24/2024] Open
Abstract
Serum or plasma is frequently utilized in biomedical research; however, its application is impeded by the requirement for invasive sample collection. The non-invasive nature of urine collection makes it an attractive alternative for disease characterization and biomarker discovery. Mass spectrometry-based protein profiling of urine has led to the discovery of several disease-associated biomarkers. Proteomic analysis of urine has not only been applied to disorders of the kidney and urinary bladder but also to conditions affecting distant organs because proteins excreted in the urine originate from multiple organs. This review provides a progress update on urinary proteomics carried out over the past decade. Studies summarized in this review have expanded the catalog of proteins detected in the urine in a variety of clinical conditions. The wide range of applications of urine analysis-from characterizing diseases to discovering predictive, diagnostic and prognostic markers-continues to drive investigations of the urinary proteome.
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Affiliation(s)
- Neha Joshi
- Manipal Academy of Higher Education (MAHE), Manipal, 576104, India
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Kishore Garapati
- Manipal Academy of Higher Education (MAHE), Manipal, 576104, India
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Vivek Ghose
- Manipal Academy of Higher Education (MAHE), Manipal, 576104, India
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India
| | - Richard K Kandasamy
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, 55905, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA
| | - Akhilesh Pandey
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India.
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA.
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, 55905, USA.
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA.
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Wu N, Xiao F, Zhang J, Chi Y, Zhai Y, Chen B, Lu J. Proteomic characteristics of plasma and blood cells in natural aging rhesus monkeys. Proteomics 2022; 22:e2200049. [PMID: 36037246 DOI: 10.1002/pmic.202200049] [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: 01/28/2022] [Revised: 07/13/2022] [Accepted: 08/09/2022] [Indexed: 12/29/2022]
Abstract
Aging has become a serious social issue that places a heavy burden on society. However, the underlying mechanisms of aging remain unclear. This study sought to understand the aging process as it may be affected by proteins in the blood, the most important functional system for material transportation in the body. We analyzed and compared the protein expression spectrums in the blood of old and young rhesus monkeys and found 257 proteins expressed differentially in plasma and 1183 proteins expressed differentially in blood cells. Through bioinformatics analysis, we found that the differentially-expressed proteins in plasma were involved in signal pathways related to complement and coagulation cascades, pertussis, malaria, phagosome, and cholesterol metabolism, while the differentially-expressed proteins in blood cells were involved in endocytosis, proteasome, ribosome, protein processing in the endoplasmic reticulum, and Parkinson's disease. We confirmed that the protein levels of complement C2 in plasma and actin-related protein 2/3 complex subunit 2 (ARPC2) in blood cells obviously decreased, whereas the complement C3 and complement component 4 binding protein beta (C4BPB) significantly increased in plasma of old rhesus monkeys and C57BL/6 mice. Our results suggest that C2, C3, C4BPB, and ARPC2 can be used as target proteins for anti-aging research.
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Affiliation(s)
- Na Wu
- Laboratory Animal Resource Center, Capital Medical University, Beijing, China.,School of Basic Medical Sciences, Beijing Key Laboratory of Neural Regeneration and Repair, Capital Medical University, Beijing, China
| | - Fuchuan Xiao
- Department of Laboratory Animal Sciences, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Jing Zhang
- Laboratory Animal Resource Center, Capital Medical University, Beijing, China.,School of Basic Medical Sciences, Beijing Key Laboratory of Neural Regeneration and Repair, Capital Medical University, Beijing, China.,Department of Laboratory Animal Sciences, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Yafei Chi
- Laboratory Animal Resource Center, Capital Medical University, Beijing, China
| | - Yanan Zhai
- Laboratory Animal Resource Center, Capital Medical University, Beijing, China
| | - Baian Chen
- Laboratory Animal Resource Center, Capital Medical University, Beijing, China.,School of Basic Medical Sciences, Beijing Key Laboratory of Neural Regeneration and Repair, Capital Medical University, Beijing, China.,Department of Laboratory Animal Sciences, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Jing Lu
- Laboratory Animal Resource Center, Capital Medical University, Beijing, China.,School of Basic Medical Sciences, Beijing Key Laboratory of Neural Regeneration and Repair, Capital Medical University, Beijing, China.,Department of Laboratory Animal Sciences, School of Basic Medical Sciences, Capital Medical University, Beijing, China
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Proteomic Studies of Blood and Vascular Wall in Atherosclerosis. Int J Mol Sci 2021; 22:ijms222413267. [PMID: 34948066 PMCID: PMC8707794 DOI: 10.3390/ijms222413267] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/02/2021] [Accepted: 12/07/2021] [Indexed: 12/12/2022] Open
Abstract
The review is devoted to the analysis of literature data related to the role of proteomic studies in the study of atherosclerotic cardiovascular diseases. Diagnosis of patients with atherosclerotic plaques before clinical manifestations is an arduous task. The review presents the results of research on the new proteomic potential biomarkers of coronary heart disease, coronary atherosclerosis, acute coronary syndrome, myocardial infarction, carotid artery atherosclerosis. Also, the analysis of literature data on proteomic studies of the vascular wall was carried out. To assess the involvement of proteins in the pathological process of atherosclerosis, it is important to investigate the specific relationships between proteins in the arteries, expression and concentration of proteins. The development of proteomic technologies has made it possible to analyse the number of proteins associated with the development of the disease. Analysis of the proteomic profile of the vascular wall in atherosclerosis can help to detect possible diagnostically significant protein structures or potential biomarkers of the disease and develop novel approaches to the diagnosis of atherosclerosis and its complications.
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Cao H, Zhu X, Chen X, Yang Y, Zhou Q, Xu W, Wang D. Quantitative proteomic analysis to identify differentially expressed proteins in the persistent atrial fibrillation using TMT coupled with nano-LC-MS/MS. Am J Transl Res 2020; 12:5032-5047. [PMID: 33042404 PMCID: PMC7540158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 08/01/2020] [Indexed: 06/11/2023]
Abstract
Persistent atrial fibrillation (PeAF) is a progressive cardiovascular disease with a high risk for most patients after diagnosis. Poor molecular description of PeAF has led to unsatisfactory interpretation of the pathogenesis of it, resulting in the lack of effective treatments. The aim of the present study was to find several new potential biomarkers for early prevention, diagnosis and treatment of this disease and explore the underlying molecular mechanisms. An absolute quantitation Tandem Mass Tag (TMT)-liquid chromatography-tandem mass spectrometry (LC-MS/MS) approach was applied to identify differentially expressed proteins (DEPs) in left atrial appendage. Totally, 4682 proteins were identified and 4159 proteins were quantified. Compared with control subjects, 118 DEPs (85 upregulated proteins and 33 downregulated proteins) were identified in the atrial tissues of PeAF patients. Using String software, a regulatory network containing 87 nodes and 244 edges was built, and the functional enrichment showed that DEPs were predominantly involved in protein digestion and absorption, regulation of metabolism and focal adhesion. Four proteins, collagen 1 (COL-I), collagen 2 (COL-II), ras-related protein 1 (RAP1) and leucine-rich alpha-2-glycoprotein 1 (LRG1) were selected for validation using Western blot analysis to distinguish PeAF patients and control subjects. The present results provide a comprehensive understanding of the pathophysiological mechanisms of PeAF and the validated biomarkers for the diagnosis of PeAF, which facilitate the development of therapeutic targets.
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Affiliation(s)
- Hailong Cao
- Department of Thoracic and Cardiovascular Surgery, The Affiliated Drum Tower Hospital of Nanjing University Medical SchoolNanjing 210008, China
| | - Xiyu Zhu
- Department of Thoracic and Cardiovascular Surgery, The Affiliated Drum Tower Hospital of Nanjing University Medical SchoolNanjing 210008, China
| | - Xin Chen
- Department of Cardiology, The Affiliated Drum Tower Hospital of Nanjing University Medical SchoolNanjing 210008, China
| | - Yining Yang
- Department of Cardiology, The Affiliated Drum Tower Hospital of Nanjing University Medical SchoolNanjing 210008, China
| | - Qing Zhou
- Department of Thoracic and Cardiovascular Surgery, The Affiliated Drum Tower Hospital of Nanjing University Medical SchoolNanjing 210008, China
| | - Wei Xu
- Department of Cardiology, The Affiliated Drum Tower Hospital of Nanjing University Medical SchoolNanjing 210008, China
| | - Dongjin Wang
- Department of Thoracic and Cardiovascular Surgery, The Affiliated Drum Tower Hospital of Nanjing University Medical SchoolNanjing 210008, China
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