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Sun J, Chang J, Guo Z, Sun H, Xu J, Liu X, Sun W. Proteomics Analysis of Renal Cell Line Caki-2 with AFMID Overexpression and Potential Biomarker Discovery in Urine. J Proteome Res 2024. [PMID: 39213636 DOI: 10.1021/acs.jproteome.4c00431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Aromatic caninurine formamase (AFMID) is an enzyme involved in the tryptophan pathway, metabolizing N-formylkynurenine to kynurenine. AFMID had been found significantly downregulated in clear cell renal cell carcinoma (ccRCC) in both tissue and urine samples. Although ccRCC is characterized by a typical Warburg-like phenotype, mitochondrial dysfunction, and elevated fat deposition, it is unknown whether AFMID plays a role in tumorigenesis and the development of ccRCC. In the present study, AFMID overexpression had inhibitory effects for ccRCC cells, decreasing the rate of cell proliferation. Quantitative proteomics showed that AFMID overexpression altered cellular signaling pathways involved in cell growth and cellular metabolism pathways, including lipid metabolism and inositol phosphate metabolism. Further urine proteomic analysis indicated that cellular function dysfunction with AFMID overexpression could be reflected in the urine. The activity of predicted upregulators DDX58, TREX1, TGFB1, SMARCA4, and TNF in ccRCC cells and urine showed opposing change trends. Potential urinary biomarkers were tentatively discovered and further validated using an independent cohort. The protein panel of APOC3, UMOD, and CILP achieved an AUC value of 0.862 for the training cohort and 0.883 for the validation cohort. The present study is of significance in terms of highlighting various aspects of pathway changes associated with AFMID enzymes, discovering potential specific biomarkers for potential patient diagnosis, and therapeutic targeting.
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Affiliation(s)
- Jiameng Sun
- Core Instrument Facility, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, 5 Dong Dan San Tiao, Beijing 100005, China
| | - Jinchun Chang
- National Institute of Biological Sciences,7 Science Park Road ZGC Life Science Park, Beijing 102206, China
- School of Health, Quanzhou Medical College, No. 2 Anji Road, Luojiang District, Quanzhou City, Fujian Province 362011, China
| | - Zhengguang Guo
- Core Instrument Facility, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, 5 Dong Dan San Tiao, Beijing 100005, China
| | - Haidan Sun
- Core Instrument Facility, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, 5 Dong Dan San Tiao, Beijing 100005, China
| | - Jiyu Xu
- Core Instrument Facility, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, 5 Dong Dan San Tiao, Beijing 100005, China
| | - Xiaoyan Liu
- Core Instrument Facility, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, 5 Dong Dan San Tiao, Beijing 100005, China
| | - Wei Sun
- Core Instrument Facility, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, 5 Dong Dan San Tiao, Beijing 100005, China
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2
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Li N, Gao Y, Zhang Y, Deng Y. An integrated multi-level analysis reveals learning-memory deficits and synaptic dysfunction in the rat model exposure to austere environment. J Proteomics 2023; 279:104887. [PMID: 36966970 DOI: 10.1016/j.jprot.2023.104887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 03/15/2023] [Accepted: 03/21/2023] [Indexed: 03/30/2023]
Abstract
Austere environment existing in tank, submarine and vessel has many risk factors including high temperature and humidity, confinement, noise, hypoxia, and high level of carbon dioxide, which may cause depression and cognitive impairment. However, the underlying mechanism is not fully understood yet. We attempt to investigate the effects of austere environment (AE) on emotion and cognitive function in a rodent model. After 21 days of AE stress, the rats exhibit depressive-like behavior and cognitive impairment. Compared with control group, the glucose metabolic level of the hippocampus is significantly decreased using whole-brain positron emission tomography (PET) imaging, and the density of dendritic spines of the hippocampus is remarkably reduced in AE group. Then, we employ a label-free quantitative proteomics strategy to investigate the differentially abundant proteins in rats' hippocampus. It is striking that the differentially abundant proteins annotated by KEGG enrich in oxidative phosphorylation pathway, synaptic vesicle cycle pathway and glutamatergic synapses pathway. The synaptic vesicle transport related proteins (Syntaxin-1A, Synaptogyrin-1 and SV-2) are down-regulated, resulting in the accumulation of intracellular glutamate. Furthermore, the concentration of hydrogen peroxide and malondialdehyde is increased while the activity of superoxide dismutase and complex I and IV of mitochondria is decreased, indicating that oxidative damage to hippocampal synapses is associated with the cognitive decline. The results of this study offer direct evidence, for the first time, that austere environment can substantially cause learning and memory deficits and synaptic dysfunction in a rodent model via behavioral assessments, PET imaging, label-free proteomics, and oxidative stress tests. SIGNIFICANCE: The incidence of depression and cognitive decline in military occupations (for example, tanker and submariner) is significantly higher than that of global population. In the present study, we first established novel model to simulate the coexisting risk factors in the austere environment. The results of this study offer the direct evidences, for the first time, that the austere environment can substantially cause learning and memory deficits by altering plasticity of the synaptic transmission in a rodent model via proteomic strategy, PET imaging, oxidative stress and behavioral assessments. These findings provide valuable information to better understand the mechanisms of cognitive impairment.
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Affiliation(s)
- Nuomin Li
- Institute of Engineering Medicine, Beijing Institute of Technology, Beijing 100081, China
| | - Yanan Gao
- Institute of Engineering Medicine, Beijing Institute of Technology, Beijing 100081, China
| | - Yongqian Zhang
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China.
| | - Yulin Deng
- Institute of Engineering Medicine, Beijing Institute of Technology, Beijing 100081, China; School of Life Science, Beijing Institute of Technology, Beijing 100081, China; Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, Beijing Institute of Technology, Beijing 100081, China.
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3
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Li N, Wang H, Xin S, Min R, Zhang Y, Deng Y. Confinement induces oxidative damage and synaptic dysfunction in mice. Front Physiol 2022; 13:999574. [PMID: 36505063 PMCID: PMC9729776 DOI: 10.3389/fphys.2022.999574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 11/10/2022] [Indexed: 11/25/2022] Open
Abstract
A confined environment is an enclosed area where entry or exit is highly restricted, which is a risk factor for a work crew's mental health. Previous studies have shown that a crew is more susceptible to developing anxiety or depression in a confined environment. However, the underlying mechanism by which negative emotion is induced by confinement is not fully understood. Hence, in this study, mice were retained in a tube to simulate short-term confinement. The mice exhibited depressive-like behavior. Additionally, the levels of H2O2 and malondialdehyde in the prefrontal cortex were significantly increased in the confinement group. Furthermore, a label-free quantitative proteomic strategy was applied to analyze the abundance of proteins in the prefrontal cortex of mice. A total of 71 proteins were considered differentially abundant proteins among 3,023 identified proteins. Two differentially abundant proteins, superoxide dismutase [Mn] and syntaxin-1A, were also validated by a parallel reaction monitoring assay. Strikingly, the differentially abundant proteins were highly enriched in the respiratory chain, oxidative phosphorylation, and the synaptic vesicle cycle, which might lead to oxidative damage and synaptic dysfunction. The results of this study provide valuable information to better understand the mechanisms of depressive-like behavior induced by confined environments.
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Affiliation(s)
- Nuomin Li
- Institute of Engineering Medicine, Beijing Institute of Technology, Beijing, China
| | - Hao Wang
- Institute of Engineering Medicine, Beijing Institute of Technology, Beijing, China
| | - Shuchen Xin
- School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Rui Min
- School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Yongqian Zhang
- School of Life Science, Beijing Institute of Technology, Beijing, China,*Correspondence: Yongqian Zhang,
| | - Yulin Deng
- Institute of Engineering Medicine, Beijing Institute of Technology, Beijing, China,School of Life Science, Beijing Institute of Technology, Beijing, China,Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, Beijing Institute of Technology, Beijing, China
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4
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Jiang J, Zhao J, Wang Y, Liu D, Zhang M. Urine inter‐alpha‐trypsin inhibitor family‐related proteins may serve as biomarkers for disease activity of lupus. J Clin Lab Anal 2022; 36:e24622. [PMID: 35870194 PMCID: PMC9459346 DOI: 10.1002/jcla.24622] [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: 04/10/2022] [Revised: 06/22/2022] [Accepted: 07/08/2022] [Indexed: 11/30/2022] Open
Abstract
Background Systemic lupus erythematosus (SLE) is a chronic inflammatory disease involving multiple tissues. Inter‐Alpha‐Trypsin Inhibitor (ITI) family proteins have a role in maintaining tissue homeostasis, but their possible clinical significance in the SLE patients has not been reported. The aim of this study was to analyze and verify the expression of ITI‐related proteins in the urine of SLE patients, further explore the features of these proteins in disease activity. Methods Based on label‐free proteomics technology and bioinformatics technology, we analyzed the expression of ITI family‐related proteins in the urine of lupus. Subsequently, Western‐blot and targeted proteomics were used to qualitatively and quantitatively verify the expression of these proteins, respectively. Results A total of seven ITI family‐related proteins were screened and identified; and six of these proteins were differentially expressed in the urine of SLE patients. Further quantitative analysis showed that the expressions of ITIH2, ECM1, and ITIH5 in urine between active SLE group and stable SLE group were consistent with the preliminary screening results. The expression of ITIH2 and ECM1 in the renal damage group were also consistent with the screening results. Moreover, ITIH2 and ECM1 have a good correlation with disease activity and have a certain correlation with renal damage. Conclusions In this exploratory study, we evaluated the expression of ITI family‐related proteins in the urine of SLE and found that urine ITIH2 and ECM1 were closely related to SLE activity, especially kidney damage, providing an experimental basis for further exploration of the potential roles in monitoring lupus and lupus nephritis activity.
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Affiliation(s)
- Jun Jiang
- Clinical Laboratory Medicine Peking University Ninth School of Clinical Medicine Beijing China
| | - Jin Zhao
- Clinical Laboratory Medicine, Beijing Shijitan Hospital Capital Medical University Beijing China
| | - Yuhua Wang
- Department of Rheumatology and Clinical Immunology, Beijing Shijitan Hospital Capital Medical University Beijing China
| | - Dan Liu
- Clinical Laboratory Medicine Peking University Ninth School of Clinical Medicine Beijing China
| | - Man Zhang
- Clinical Laboratory Medicine Peking University Ninth School of Clinical Medicine Beijing China
- Clinical Laboratory Medicine, Beijing Shijitan Hospital Capital Medical University Beijing China
- Beijing Key Laboratory of Urinary Cellular Molecular Diagnostics Beijing China
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Erozenci LA, Piersma SR, Pham TV, Bijnsdorp IV, Jimenez CR. Longitudinal stability of urinary extracellular vesicle protein patterns within and between individuals. Sci Rep 2021; 11:15629. [PMID: 34341426 PMCID: PMC8329217 DOI: 10.1038/s41598-021-95082-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 06/29/2021] [Indexed: 02/07/2023] Open
Abstract
The protein content of urinary extracellular vesicles (EVs) is considered to be an attractive non-invasive biomarker source. However, little is known about the consistency and variability of urinary EV proteins within and between individuals over a longer time-period. Here, we evaluated the stability of the urinary EV proteomes of 8 healthy individuals at 9 timepoints over 6 months using data-independent-acquisition mass spectrometry. The 1802 identified proteins had a high correlation amongst all samples, with 40% of the proteome detected in every sample and 90% detected in more than 1 individual at all timepoints. Unsupervised analysis of top 10% most variable proteins yielded person-specific profiles. The core EV-protein-interaction network of 516 proteins detected in all measured samples revealed sub-clusters involved in the biological processes of G-protein signaling, cytoskeletal transport, cellular energy metabolism and immunity. Furthermore, gender-specific expression patterns were detected in the urinary EV proteome. Our findings indicate that the urinary EV proteome is stable in longitudinal samples of healthy subjects over a prolonged time-period, further underscoring its potential for reliable non-invasive diagnostic/prognostic biomarkers.
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Affiliation(s)
- Leyla A Erozenci
- Department of Medical Oncology, OncoProteomics Laboratory, Cancer Center Amsterdam, Amsterdam UMC, Location VUMC, Amsterdam, The Netherlands
- Department of Urology, Amsterdam UMC, Location VUMC, Amsterdam, The Netherlands
| | - Sander R Piersma
- Department of Medical Oncology, OncoProteomics Laboratory, Cancer Center Amsterdam, Amsterdam UMC, Location VUMC, Amsterdam, The Netherlands
| | - Thang V Pham
- Department of Medical Oncology, OncoProteomics Laboratory, Cancer Center Amsterdam, Amsterdam UMC, Location VUMC, Amsterdam, The Netherlands
| | - Irene V Bijnsdorp
- Department of Medical Oncology, OncoProteomics Laboratory, Cancer Center Amsterdam, Amsterdam UMC, Location VUMC, Amsterdam, The Netherlands.
- Department of Urology, Amsterdam UMC, Location VUMC, Amsterdam, The Netherlands.
| | - Connie R Jimenez
- Department of Medical Oncology, OncoProteomics Laboratory, Cancer Center Amsterdam, Amsterdam UMC, Location VUMC, Amsterdam, The Netherlands.
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Zhao Y, Li Y, Liu W, Xing S, Wang D, Chen J, Sun L, Mu J, Liu W, Xing B, Sun W, He F. Identification of noninvasive diagnostic biomarkers for hepatocellular carcinoma by urinary proteomics. J Proteomics 2020; 225:103780. [PMID: 32298775 DOI: 10.1016/j.jprot.2020.103780] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 04/02/2020] [Accepted: 04/11/2020] [Indexed: 02/07/2023]
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7
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Park J, Oh HJ, Han D, Wang JI, Park IA, Ryu HS, Kim Y. Parallel Reaction Monitoring-Mass Spectrometry (PRM-MS)-Based Targeted Proteomic Surrogates for Intrinsic Subtypes in Breast Cancer: Comparative Analysis with Immunohistochemical Phenotypes. J Proteome Res 2019; 19:2643-2653. [DOI: 10.1021/acs.jproteome.9b00490] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Joonho Park
- Department of Biomedical Engineering, Seoul National University College of Medicine, 103 Daehak-ro, Seoul 03080, Korea
| | - Hyeon Jeong Oh
- Department of Pathology, Seoul National University Hospital, 101 Daehak-ro, Seoul 03080, Korea
| | - Dohyun Han
- Biomedical Research Institute, Seoul National University Hospital, 101 Daehak-ro, Seoul 03080, Korea
| | - Joseph I. Wang
- Biomedical Research Institute, Seoul National University Hospital, 101 Daehak-ro, Seoul 03080, Korea
| | - In Ae Park
- Department of Pathology, Seoul National University Hospital, 101 Daehak-ro, Seoul 03080, Korea
| | - Han Suk Ryu
- Department of Pathology, Seoul National University Hospital, 101 Daehak-ro, Seoul 03080, Korea
| | - Youngsoo Kim
- Department of Biomedical Engineering, Seoul National University College of Medicine, 103 Daehak-ro, Seoul 03080, Korea
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8
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Brzhozovskiy AG, Kononikhin AS, Pastushkova LC, Kashirina DN, Indeykina MI, Popov IA, Custaud MA, Larina IM, Nikolaev EN. The Effects of Spaceflight Factors on the Human Plasma Proteome, Including Both Real Space Missions and Ground-Based Experiments. Int J Mol Sci 2019; 20:E3194. [PMID: 31261866 PMCID: PMC6651200 DOI: 10.3390/ijms20133194] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 06/05/2019] [Accepted: 06/25/2019] [Indexed: 01/07/2023] Open
Abstract
The aim of the study was to compare proteomic data on the effects of spaceflight factors on the human body, including both real space missions and ground-based experiments. LC-MS/MS-based proteomic analysis of blood plasma samples obtained from 13 cosmonauts before and after long-duration (169-199 days) missions on the International Space Station (ISS) and for five healthy men included in 21-day-long head-down bed rest (HDBR) and dry immersion experiments were performed. The semi-quantitative label-free analysis revealed significantly changed proteins: 19 proteins were significantly different on the first (+1) day after landing with respect to background levels; 44 proteins significantly changed during HDBR and 31 changed in the dry immersion experiment. Comparative analysis revealed nine common proteins (A1BG, A2M, SERPINA1, SERPINA3, SERPING1, SERPINC1, HP, CFB, TF), which changed their levels after landing, as well as in both ground-based experiments. Common processes, such as platelet degranulation, hemostasis, post-translational protein phosphorylation and processes of protein metabolism, indicate common pathogenesis in ground experiments and during spaceflight. Dissimilarity in the lists of significantly changed proteins could be explained by the differences in the dynamics of effective development in the ground-based experiments. Data are available via ProteomeXchange using the identifier PXD013305.
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Affiliation(s)
- Alexander G Brzhozovskiy
- Institute of Biomedical Problems, Russian Federation State Scientific Research Center, Russian Academy of Sciences, 119991 Moscow, Russia
- Laboratory of mass spectrometry, CDISE, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
| | - Alexey S Kononikhin
- Institute of Biomedical Problems, Russian Federation State Scientific Research Center, Russian Academy of Sciences, 119991 Moscow, Russia
- Laboratory of mass spectrometry, CDISE, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
| | - Lyudmila Ch Pastushkova
- Institute of Biomedical Problems, Russian Federation State Scientific Research Center, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Daria N Kashirina
- Institute of Biomedical Problems, Russian Federation State Scientific Research Center, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Maria I Indeykina
- V.L. Talrose Institute for Energy Problems of Chemical Physics, N.N. Semenov Federal Center of Chemical Physic of RAS, 119334 Moscow, Russia
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Igor A Popov
- V.L. Talrose Institute for Energy Problems of Chemical Physics, N.N. Semenov Federal Center of Chemical Physic of RAS, 119334 Moscow, Russia
- Laboratory of Ion and Molecular Physics, Moscow Institute of Physics and Technology, Dolgoprudny, 141701 Moscow, Russia
| | | | - Irina M Larina
- Institute of Biomedical Problems, Russian Federation State Scientific Research Center, Russian Academy of Sciences, 119991 Moscow, Russia.
- Laboratory of Ion and Molecular Physics, Moscow Institute of Physics and Technology, Dolgoprudny, 141701 Moscow, Russia.
| | - Evgeny N Nikolaev
- Laboratory of mass spectrometry, CDISE, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia.
- V.L. Talrose Institute for Energy Problems of Chemical Physics, N.N. Semenov Federal Center of Chemical Physic of RAS, 119334 Moscow, Russia.
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Shao C, Zhao M, Chen X, Sun H, Yang Y, Xiao X, Guo Z, Liu X, Lv Y, Chen X, Sun W, Wu D, Gao Y. Comprehensive Analysis of Individual Variation in the Urinary Proteome Revealed Significant Gender Differences. Mol Cell Proteomics 2019; 18:1110-1122. [PMID: 30894400 PMCID: PMC6553935 DOI: 10.1074/mcp.ra119.001343] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Revised: 03/15/2019] [Indexed: 12/15/2022] Open
Abstract
Disease biomarkers are the measurable changes associated with a pathophysiological process. Without homeostatic control, urine accumulates systematic changes in the body. Thus, urine is an attractive biological material for the discovery of disease biomarkers. One of the major bottlenecks in urinary biomarker discovery is that the concentration and composition of urinary proteins are influenced by many physiological factors. To elucidate the individual variation and related factors influencing the urinary proteome, we comprehensively analyzed the urine samples from healthy adult donors (aged 20-69 years). Co-expression network analysis revealed protein clusters representing the metabolic status, gender-related differences and age-related differences in urinary proteins. In particular, we demonstrated that gender is a crucial factor contributing to individual variation. Proteins that were increased in the male urine samples include prostate-secreted proteins and TIMP1, a protein whose abundance alters under various cancers and renal diseases; however, the proteins that were increased in the female urine samples have known functions in the immune system. Nine gender-related proteins were validated on 85 independent samples by multiple reaction monitoring. Five of these proteins were further used to build a model that could accurately distinguish male and female urine samples with an area under curve value of 0.94. Based on the above results, we strongly suggest that future biomarker investigations should consider gender as a crucial factor in experimental design and data analysis. Finally, reference intervals of each urinary protein were estimated, providing a baseline for the discovery of abnormalities.
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Affiliation(s)
- Chen Shao
- From the ‡Center for Bioinformatics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China
- §State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences(Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Mindi Zhao
- ¶Department of Laboratory Medicine, Beijing Hospital, National Center of Gerontology, Beijing, 100730, China
- ‖Department of Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College
| | - Xizhao Chen
- **Department of Nephrology, Chinese PLA General Hospital, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing, China
| | - Haidan Sun
- ‡‡Core Facility of Instrument, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College
| | - Yehong Yang
- ‡‡Core Facility of Instrument, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College
| | - Xiaoping Xiao
- ‡‡Core Facility of Instrument, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College
- §§Cytology Lab, Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
| | - Zhengguang Guo
- ‡‡Core Facility of Instrument, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College
| | - Xiaoyan Liu
- ‡‡Core Facility of Instrument, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College
| | - Yang Lv
- **Department of Nephrology, Chinese PLA General Hospital, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing, China
| | - Xiangmei Chen
- **Department of Nephrology, Chinese PLA General Hospital, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing, China
| | - Wei Sun
- ‡‡Core Facility of Instrument, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College;
| | - Di Wu
- **Department of Nephrology, Chinese PLA General Hospital, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing, China;
| | - Youhe Gao
- ¶¶Department of Biochemistry and Molecular Biology, Beijing Normal University, Gene Engineering Drug and Biotechnology Beijing Key Laboratory, Beijing, China
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Chen YT, Tsai CH, Chen CL, Yu JS, Chang YH. Development of biomarkers of genitourinary cancer using mass spectrometry-based clinical proteomics. J Food Drug Anal 2019; 27:387-403. [PMID: 30987711 PMCID: PMC9296213 DOI: 10.1016/j.jfda.2018.09.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 09/19/2018] [Accepted: 09/20/2018] [Indexed: 12/23/2022] Open
Abstract
Prostate, bladder and kidney cancer are the three most common types of genitourinary cancer in the world. Of these, prostate and bladder cancers are within the top 10 most common cancers in men. Notably, kidney cancer causes no obvious symptoms in the early stages. To satisfy clinical-management requirements, researchers have developed numerous biomarkers by applying proteomic approaches using clinical serum, urine and tissue specimens, as well as cell and animal models. Through application of biomarker pipeline protocols, including discovery, verification and validation phases, and mass-spectrometric based proteomic platforms coupled with multiplexed quantification assays, these studies have led to recent rapid progress in this area. With improvements in mass-spectrometric based proteomic techniques, numerous promising biomarker candidates and marker panels for various clinical purposes have been proposed. Verification of novel protein biomarker candidates is very resource demanding (e.g. on the clinical and laboratory sides). With the support of national consortia, it is now possible to investigate the future clinical use of such biomarker strategies and assess their cost-effectiveness in personalized medicine.
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Affiliation(s)
- Yi-Ting Chen
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan,
Taiwan
- Molecular Medicine Research Center, College of Medicine, Chang Gung University, Taoyuan,
Taiwan
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan,
Taiwan
- Department of Nephrology, Chang Gung Memorial Hospital, Linkou Medical Center, Taiwan University, Taoyuan,
Taiwan
- Corresponding author. Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Cheng-Han Tsai
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan,
Taiwan
| | - Chien-Lun Chen
- Department of Urology, Chang Gung Memorial Hospital, Taoyuan,
Taiwan
- College of Medicine, Chang Gung University, Taoyuan,
Taiwan
| | - Jau-Song Yu
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan,
Taiwan
- Molecular Medicine Research Center, College of Medicine, Chang Gung University, Taoyuan,
Taiwan
- Liver Research Center, Chang Gung Memorial Hospital, Linkou,
Taiwan
| | - Ying-Hsu Chang
- Division of Urology, Department of Surgery, LinKou Chang Gung Memorial Hospital, Taoyuan,
Taiwan
- Graduate Institute of Clinical Medical Sciences, College of Medicine, Chang Gung University, Taoyuan,
Taiwan
- Corresponding author. Division of Urology, Department of Surgery, LinKou Chang Gung Memorial Hospital, Taoyuan, Taiwan. E-mail addresses: (Y.-T. Chen), (Y.-H. Chang)
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11
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Chen S, Yang CT, Downs ML. Detection of Six Commercially Processed Soy Ingredients in an Incurred Food Matrix Using Parallel Reaction Monitoring. J Proteome Res 2019; 18:995-1005. [PMID: 30704242 DOI: 10.1021/acs.jproteome.8b00689] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Soybeans are one of the major allergenic foods in many countries. Soybeans are commonly processed into different types of soy ingredients to achieve the desired properties. The processing, however, may affect the protein profiles and protein structure, thus affecting the detection of soy proteins. Mass spectrometry (MS) is a potential alternative to the traditional immunoassays for the detection of soy-derived ingredients in foods. This study aims to develop a liquid chromatography-tandem MS method that uniformly detects different types of soy-derived ingredients. Target peptides applicable to the detection of six commercial soy ingredients were identified based on the results of MS label-free quantification and a set of selection criteria. The results indicated that soy ingredient processing can result in different protein profiles. A total of six soy ingredients were then individually incurred into cookie matrices at different levels. Sample preparation methods were optimized, and a distinct improvement in peptide performance was observed after optimization. Cookies and dough incurred with different soy ingredients at 100 ppm total soy protein showed a similar level of peptide recovery (90% mean signal relative to unroasted soy flour), demonstrating the ability of the MS method to detect processed soy ingredients in a uniform manner.
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Affiliation(s)
- Shimin Chen
- Food Allergy Research and Resource Program, Department of Food Science and Technology , University of Nebraska , Lincoln , Nebraska 68588 , United States
| | - Charles T Yang
- Thermo Fisher Scientific , San Jose , California 95134 , United States
| | - Melanie L Downs
- Food Allergy Research and Resource Program, Department of Food Science and Technology , University of Nebraska , Lincoln , Nebraska 68588 , United States
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12
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Harpole M, Davis J, Espina V. Current state of the art for enhancing urine biomarker discovery. Expert Rev Proteomics 2017; 13:609-26. [PMID: 27232439 DOI: 10.1080/14789450.2016.1190651] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
INTRODUCTION Urine is a highly desirable biospecimen for biomarker analysis because it can be collected recurrently by non-invasive techniques, in relatively large volumes. Urine contains cellular elements, biochemicals, and proteins derived from glomerular filtration of plasma, renal tubule excretion, and urogenital tract secretions that reflect, at a given time point, an individual's metabolic and pathophysiologic state. AREAS COVERED High-resolution mass spectrometry, coupled with state of the art fractionation systems are revealing the plethora of diagnostic/prognostic proteomic information existing within urinary exosomes, glycoproteins, and proteins. Affinity capture pre-processing techniques such as combinatorial peptide ligand libraries and biomarker harvesting hydrogel nanoparticles are enabling measurement/identification of previously undetectable urinary proteins. Expert commentary: Future challenges in the urinary proteomics field include a) defining either single or multiple, universally applicable data normalization methods for comparing results within and between individual patients/data sets, and b) defining expected urinary protein levels in healthy individuals.
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Affiliation(s)
- Michael Harpole
- a Center for Applied Proteomics and Molecular Medicine , George Mason University , Manassas , VA , USA
| | - Justin Davis
- b Department of Chemistry/Biochemistry , George Mason University , Manassas , VA , USA
| | - Virginia Espina
- a Center for Applied Proteomics and Molecular Medicine , George Mason University , Manassas , VA , USA
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13
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Woo J, Han D, Wang JI, Park J, Kim H, Kim Y. Quantitative Proteomics Reveals Temporal Proteomic Changes in Signaling Pathways during BV2 Mouse Microglial Cell Activation. J Proteome Res 2017; 16:3419-3432. [DOI: 10.1021/acs.jproteome.7b00445] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
| | - Dohyun Han
- Proteomics
Core Facility, Biomedical Research Institute, Seoul National University Hospital, 101 Daehangro, Seoul 110-799, Korea
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14
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Brzhozovskiy A, Kononikhin A, Indeykina M, Pastushkova LK, Popov IA, Nikolaev EN, Larina IM. Label-free study of cosmonaut's urinary proteome changes after long-duration spaceflights. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2017; 23:225-229. [PMID: 29028400 DOI: 10.1177/1469066717717610] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
During the entire time that cosmonauts stay on board the international space station, different extreme space flight factors affect their bodies. In order to find out what physiological changes occur under the influence of spaceflight, different parameters of the human body before and after flights are monitored. Analysis of the urine proteome is one of the most perspective non-invasive methods of condition monitoring. The aim of the study was to perform a comparative semi-quantitative label-free urine proteome analysis of samples collected from 21 cosmonauts before and after long-duration spaceflight at the international space station. For proteomic analysis, urine samples were collected from cosmonauts at three time periods: six months prior to the flight as a background, and on days 1 and 7 of the recovery period after landing. All probes were analyzed by LC-MS/MS, and 256 proteins were identified with more than one unique peptide. The core proteome consists of 50 proteins that are detected in more than 70% of the samples. Label-free semi-quantitative analysis enables us to find 20 proteins which were significantly changed on +1 day and +7 day with respect to background. Most of these proteins participate in the regulation of biological processes, in the regulation of the immune system and in intracellular processes also; some of these proteins are related with stress and response to stimulus. In conclusion, the proteomic analysis of cosmonauts' urine samples provides new data on the human body's adaptation to ground conditions after long-duration spaceflight.
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Affiliation(s)
- A Brzhozovskiy
- 1 Institute of Biomedical Problems - Russian Federation State Scientific Research Center, Russian Academy of Sciences, Moscow, Russia
| | - A Kononikhin
- 1 Institute of Biomedical Problems - Russian Federation State Scientific Research Center, Russian Academy of Sciences, Moscow, Russia
- 2 Moscow Institute of Physics and Technology, Moscow, Russia
- 3 V.L. Talrose Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - M Indeykina
- 3 V.L. Talrose Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
- 4 Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - LKh Pastushkova
- 1 Institute of Biomedical Problems - Russian Federation State Scientific Research Center, Russian Academy of Sciences, Moscow, Russia
| | - I A Popov
- 2 Moscow Institute of Physics and Technology, Moscow, Russia
- 3 V.L. Talrose Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - E N Nikolaev
- 3 V.L. Talrose Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
- 4 Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
- 5 Skolkovo Institute of Science and Technology, Space Cluster, Skolkovo, Russia
| | - I M Larina
- 1 Institute of Biomedical Problems - Russian Federation State Scientific Research Center, Russian Academy of Sciences, Moscow, Russia
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15
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Leng W, Ni X, Sun C, Lu T, Malovannaya A, Jung SY, Huang Y, Qiu Y, Sun G, Holt MV, Ding C, Sun W, Men X, Shi T, Zhu W, Wang Y, He F, Zhen B, Wang G, Qin J. Proof-of-Concept Workflow for Establishing Reference Intervals of Human Urine Proteome for Monitoring Physiological and Pathological Changes. EBioMedicine 2017; 18:300-310. [PMID: 28396014 PMCID: PMC5405183 DOI: 10.1016/j.ebiom.2017.03.028] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 03/20/2017] [Accepted: 03/20/2017] [Indexed: 12/24/2022] Open
Abstract
Urine as a true non-invasive sampling source holds great potential for biomarker discovery. While approximately 2000 proteins can be detected by mass spectrometry in urine from healthy people, the amount of these proteins vary considerably. A systematic evaluation of a large number of samples is needed to determine the range of the variations. Current biomarker studies often measure limited number of urine samples in the discovery phase, which makes it difficult to determine whether proteins differentially expressed between control and disease groups represent actual difference, or are just physiological variations among the individuals, leads to failures in the validation phase with the increased sample numbers. Here, we report a streamlined workflow with capacity of measuring 8 urine proteomes per day at the coverage of >1500 proteins. With this workflow, we evaluated variations in 497 urine proteomes from 167 healthy donors, establishing reference intervals (RIs) that covered urine protein variations. We demonstrated that RIs could be used to monitor physiological changes by detecting transient outlier proteins. Furthermore, we provided a RIs-based algorithm for biomarker discovery and validation to screen for diseases such as cancer. This study provided a proof-of-principle workflow for the use of urine proteome for health monitoring and disease screening.
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Affiliation(s)
- Wenchuan Leng
- State Key Laboratory of Proteomics, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing Proteome Research Center, Beijing 102206, China
| | - Xiaotian Ni
- State Key Laboratory of Proteomics, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing Proteome Research Center, Beijing 102206, China; Center for Bioinformatics, East China Normal University, Shanghai 200241, China
| | - Changqing Sun
- Joint Center for Translational Medicine, Tianjin Baodi Hospital, Tianjin 301800, China
| | - Tianyuan Lu
- State Key Laboratory of Proteomics, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing Proteome Research Center, Beijing 102206, China
| | - Anna Malovannaya
- Alkek Center for Molecular Discovery, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sung Yun Jung
- Alkek Center for Molecular Discovery, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yin Huang
- State Key Laboratory of Proteomics, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing Proteome Research Center, Beijing 102206, China; School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Yang Qiu
- State Key Laboratory of Proteomics, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing Proteome Research Center, Beijing 102206, China
| | - Guannan Sun
- State Key Laboratory of Proteomics, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing Proteome Research Center, Beijing 102206, China
| | - Matthew V Holt
- Alkek Center for Molecular Discovery, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Chen Ding
- State Key Laboratory of Proteomics, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing Proteome Research Center, Beijing 102206, China; Joint Center for Translational Medicine, Tianjin Baodi Hospital, Tianjin 301800, China
| | - Wei Sun
- State Key Laboratory of Proteomics, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing Proteome Research Center, Beijing 102206, China
| | - Xuebo Men
- Joint Center for Translational Medicine, Tianjin Baodi Hospital, Tianjin 301800, China
| | - Tieliu Shi
- Center for Bioinformatics, East China Normal University, Shanghai 200241, China
| | - Weimin Zhu
- State Key Laboratory of Proteomics, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing Proteome Research Center, Beijing 102206, China; Joint Center for Translational Medicine, Tianjin Baodi Hospital, Tianjin 301800, China
| | - Yi Wang
- Alkek Center for Molecular Discovery, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Fuchu He
- State Key Laboratory of Proteomics, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing Proteome Research Center, Beijing 102206, China
| | - Bei Zhen
- State Key Laboratory of Proteomics, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing Proteome Research Center, Beijing 102206, China; Joint Center for Translational Medicine, Tianjin Baodi Hospital, Tianjin 301800, China.
| | - Guangshun Wang
- Joint Center for Translational Medicine, Tianjin Baodi Hospital, Tianjin 301800, China.
| | - Jun Qin
- State Key Laboratory of Proteomics, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing Proteome Research Center, Beijing 102206, China; Joint Center for Translational Medicine, Tianjin Baodi Hospital, Tianjin 301800, China; Alkek Center for Molecular Discovery, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA.
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16
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Kononikhin AS, Starodubtseva NL, Pastushkova LK, Kashirina DN, Fedorchenko KY, Brhozovsky AG, Popov IA, Larina IM, Nikolaev EN. Spaceflight induced changes in the human proteome. Expert Rev Proteomics 2016; 14:15-29. [PMID: 27817217 DOI: 10.1080/14789450.2017.1258307] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
INTRODUCTION Spaceflight is one of the most extreme conditions encountered by humans: Individuals are exposed to radiation, microgravity, hypodynamia, and will experience isolation. A better understanding of the molecular processes induced by these factors may allow us to develop personalized countermeasures to minimize risks to astronauts. Areas covered: This review is a summary of literature searches from PubMed, NASA, Roskosmos and the authors' research experiences and opinions. The review covers the available proteomic data on the effects of spaceflight factors on the human body, including both real space missions and ground-based model experiments. Expert commentary: Overall, the authors believe that the present background, methodology and equipment improvements will enhance spaceflight safety and support accumulation of new knowledge on how organisms adapt to extreme conditions.
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Affiliation(s)
- Alexey S Kononikhin
- a Institute of Biomedical Problems - Russian Federation State Scientific Research Center, Laboratory of proteomics , Russian Academy of Sciences , Moscow , Russia.,b Moscow Institute of Physics and Technology , Laboratory of ion and molecular physics , Moscow , Russia.,d V.L. Talrose Institute for Energy Problems of Chemical Physics , Laboratory of ion and molecular physics, Russian Academy of Sciences , Moscow , Russia
| | - Natalia L Starodubtseva
- b Moscow Institute of Physics and Technology , Laboratory of ion and molecular physics , Moscow , Russia.,c V. I. Kulakov Research Center for Obstetrics, Gynecology and Perinatology , Laboratory of proteomics and metabolomics, Ministry of Healthcare of the Russian Federation , Moscow , Russia.,d V.L. Talrose Institute for Energy Problems of Chemical Physics , Laboratory of ion and molecular physics, Russian Academy of Sciences , Moscow , Russia
| | - Lyudmila Kh Pastushkova
- a Institute of Biomedical Problems - Russian Federation State Scientific Research Center, Laboratory of proteomics , Russian Academy of Sciences , Moscow , Russia
| | - Daria N Kashirina
- a Institute of Biomedical Problems - Russian Federation State Scientific Research Center, Laboratory of proteomics , Russian Academy of Sciences , Moscow , Russia
| | | | - Alexander G Brhozovsky
- a Institute of Biomedical Problems - Russian Federation State Scientific Research Center, Laboratory of proteomics , Russian Academy of Sciences , Moscow , Russia
| | - Igor A Popov
- b Moscow Institute of Physics and Technology , Laboratory of ion and molecular physics , Moscow , Russia.,c V. I. Kulakov Research Center for Obstetrics, Gynecology and Perinatology , Laboratory of proteomics and metabolomics, Ministry of Healthcare of the Russian Federation , Moscow , Russia.,d V.L. Talrose Institute for Energy Problems of Chemical Physics , Laboratory of ion and molecular physics, Russian Academy of Sciences , Moscow , Russia
| | - Irina M Larina
- a Institute of Biomedical Problems - Russian Federation State Scientific Research Center, Laboratory of proteomics , Russian Academy of Sciences , Moscow , Russia
| | - Evgeny N Nikolaev
- d V.L. Talrose Institute for Energy Problems of Chemical Physics , Laboratory of ion and molecular physics, Russian Academy of Sciences , Moscow , Russia.,e Emanuel Institute for Biochemical Physics , Russian Academy of Sciences , Moscow , Russia.,f Skolkovo Institute of Science and Technology, Space Cluster , Skolkovo , Russia
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17
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Lesur A, Gallien S, Domon B. Hyphenation of fast liquid chromatography with high-resolution mass spectrometry for quantitative proteomics analyses. Trends Analyt Chem 2016. [DOI: 10.1016/j.trac.2016.01.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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18
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Holman SW, Hammond DE, Simpson DM, Waters J, Hurst JL, Beynon RJ. Protein turnover measurement using selected reaction monitoring-mass spectrometry (SRM-MS). PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2016; 374:rsta.2015.0362. [PMID: 27644981 PMCID: PMC5031629 DOI: 10.1098/rsta.2015.0362] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 06/23/2016] [Indexed: 05/28/2023]
Abstract
Protein turnover represents an important mechanism in the functioning of cells, with deregulated synthesis and degradation of proteins implicated in many diseased states. Therefore, proteomics strategies to measure turnover rates with high confidence are of vital importance to understanding many biological processes. In this study, the more widely used approach of non-targeted precursor ion signal intensity (MS1) quantification is compared with selected reaction monitoring (SRM), a data acquisition strategy that records data for specific peptides, to determine if improved quantitative data would be obtained using a targeted quantification approach. Using mouse liver as a model system, turnover measurement of four tricarboxylic acid cycle proteins was performed using both MS1 and SRM quantification strategies. SRM outperformed MS1 in terms of sensitivity and selectivity of measurement, allowing more confident determination of protein turnover rates. SRM data are acquired using cheaper and more widely available tandem quadrupole mass spectrometers, making the approach accessible to a larger number of researchers than MS1 quantification, which is best performed on high mass resolution instruments. SRM acquisition is ideally suited to focused studies where the turnover of tens of proteins is measured, making it applicable in determining the dynamics of proteins complexes and complete metabolic pathways.This article is part of the themed issue 'Quantitative mass spectrometry'.
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Affiliation(s)
- Stephen W Holman
- Centre for Proteome Research, Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
| | - Dean E Hammond
- Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Crown Street, Liverpool L69 3BX, UK
| | - Deborah M Simpson
- Centre for Proteome Research, Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
| | - John Waters
- Mammalian Behaviour and Evolution Group, Department of Evolution, Ecology and Behaviour, Institute of Integrative Biology, University of Liverpool, Leahurst Campus, Neston CH64 7TE, UK
| | - Jane L Hurst
- Mammalian Behaviour and Evolution Group, Department of Evolution, Ecology and Behaviour, Institute of Integrative Biology, University of Liverpool, Leahurst Campus, Neston CH64 7TE, UK
| | - Robert J Beynon
- Centre for Proteome Research, Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
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19
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Bourmaud A, Gallien S, Domon B. Parallel reaction monitoring using quadrupole-Orbitrap mass spectrometer: Principle and applications. Proteomics 2016; 16:2146-59. [PMID: 27145088 DOI: 10.1002/pmic.201500543] [Citation(s) in RCA: 205] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 03/21/2016] [Accepted: 05/02/2016] [Indexed: 12/19/2022]
Abstract
Targeted mass spectrometry-based approaches are nowadays widely used for quantitative proteomics studies and more recently have been implemented on high resolution/accurate mass (HRAM) instruments resulting in a considerable performance improvement. More specifically, the parallel reaction monitoring technique (PRM) performed on quadrupole-Orbitrap mass spectrometers, leveraging the high resolution and trapping capabilities of the instrument, offers a clear advantage over the conventional selected reaction monitoring (SRM) measurements executed on triple quadrupole instruments. Analyses performed in HRAM mode allow for an improved discrimination between signals derived from analytes and those resulting from matrix interferences translating in the reliable quantification of low abundance components. The purpose of the study defines various implementation schemes of PRM, namely: (i) exploratory experiments assessing the detectability of very large sets of peptides (100-1000), (ii) wide-screen analyses using (crude) internal standards to obtain statistically meaningful (relative) quantitative analyses, and (iii) precise/accurate quantification of a limited number of analytes using calibrated internal standards. Each of the three implementation schemes requires specific acquisition methods with defined parameters to appropriately control the acquisition during the actual peptide elution. This tutorial describes the different PRM approaches and discusses their benefits and limitations in terms of quantification performance and confidence in analyte identification.
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Affiliation(s)
- Adele Bourmaud
- Luxembourg Clinical Proteomics Center, Luxembourg Institute of Health (LIH), Strassen, Luxembourg.,Doctoral School in Systems and Molecular Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Sebastien Gallien
- Luxembourg Clinical Proteomics Center, Luxembourg Institute of Health (LIH), Strassen, Luxembourg
| | - Bruno Domon
- Luxembourg Clinical Proteomics Center, Luxembourg Institute of Health (LIH), Strassen, Luxembourg.,Doctoral School in Systems and Molecular Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
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20
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Santucci L, Bruschi M, Candiano G, Lugani F, Petretto A, Bonanni A, Ghiggeri GM. Urine Proteome Biomarkers in Kidney Diseases. I. Limits, Perspectives, and First Focus on Normal Urine. Biomark Insights 2016; 11:41-8. [PMID: 26997865 PMCID: PMC4795486 DOI: 10.4137/bmi.s26229] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 12/29/2015] [Accepted: 12/30/2015] [Indexed: 11/05/2022] Open
Abstract
Urine proteome is a potential source of information in renal diseases, and it is considered a natural area of investigation for biomarkers. Technology developments have markedly increased the power analysis on urinary proteins, and it is time to confront methodologies and results of major studies on the topics. This is a first part of a series of reviews that will focus on the urine proteome as a site for detecting biomarkers of renal diseases; the theme of the first review concerns methodological aspects applied to normal urine. Main issues are techniques for urine pretreatment, separation of exosomes, use of combinatorial peptide ligand libraries, mass spectrometry approaches, and analysis of data sets. Available studies show important differences, suggesting a major confounding effect of the technologies utilized for analysis. The objective is to obtain consensus about which approaches should be utilized for studying urine proteome in renal diseases.
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Affiliation(s)
- Laura Santucci
- Laboratory on Physiopathology of Uremia, Istituto Giannina Gaslini, Genova, Italy
| | - Maurizio Bruschi
- Laboratory on Physiopathology of Uremia, Istituto Giannina Gaslini, Genova, Italy
| | - Giovanni Candiano
- Laboratory on Physiopathology of Uremia, Istituto Giannina Gaslini, Genova, Italy
| | - Francesca Lugani
- Nephrology, Dialysis and Transplantation, Istituto Giannina Gaslini, Genova, Italy
| | - Andrea Petretto
- Laboratory of Mass Spectrometry - Core Facility, Istituto Giannina Gaslini, Genova, Italy
| | - Alice Bonanni
- Nephrology, Dialysis and Transplantation, Istituto Giannina Gaslini, Genova, Italy
| | - Gian Marco Ghiggeri
- Laboratory on Physiopathology of Uremia, Istituto Giannina Gaslini, Genova, Italy.; Nephrology, Dialysis and Transplantation, Istituto Giannina Gaslini, Genova, Italy
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21
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Rauniyar N. Parallel Reaction Monitoring: A Targeted Experiment Performed Using High Resolution and High Mass Accuracy Mass Spectrometry. Int J Mol Sci 2015; 16:28566-81. [PMID: 26633379 PMCID: PMC4691067 DOI: 10.3390/ijms161226120] [Citation(s) in RCA: 223] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 11/24/2015] [Accepted: 11/25/2015] [Indexed: 12/22/2022] Open
Abstract
The parallel reaction monitoring (PRM) assay has emerged as an alternative method of targeted quantification. The PRM assay is performed in a high resolution and high mass accuracy mode on a mass spectrometer. This review presents the features that make PRM a highly specific and selective method for targeted quantification using quadrupole-Orbitrap hybrid instruments. In addition, this review discusses the label-based and label-free methods of quantification that can be performed with the targeted approach.
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Affiliation(s)
- Navin Rauniyar
- W.M. Keck Foundation Biotechnology Resource Laboratory, School of Medicine, Yale University, 300 George Street, New Haven, CT 06511, USA.
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06520, USA.
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