1
|
Rhode H, Muckova P, Büchler R, Wendler S, Tautkus B, Vogel M, Moore T, Grosskreutz J, Klemm A, Nabity M. A next generation setup for pre-fractionation of non-denatured proteins reveals diverse albumin proteoforms each carrying several post-translational modifications. Sci Rep 2019; 9:11733. [PMID: 31409882 PMCID: PMC6692309 DOI: 10.1038/s41598-019-48278-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 07/29/2019] [Indexed: 02/07/2023] Open
Abstract
Proteomic biomarker search requires the greatest analytical reproducibility and detailed information on altered proteoforms. Our protein pre-fractionation applies orthogonal native chromatography and conserves important features of protein variants such as native molecular weight, charge and major glycans. Moreover, we maximized reproducibility of sample pre-fractionation and preparation before mass spectrometry by parallelization and automation. In blood plasma and cerebrospinal fluid (CSF), most proteins, including candidate biomarkers, distribute into a multitude of chromatographic clusters. Plasma albumin, for example, divides into 15-17 clusters. As an example of our technique, we analyzed these albumin clusters from healthy volunteers and from dogs and identified cluster-typical modification patterns. Renal disease further modifies these patterns. In human CSF, we found only a subset of proteoforms with fewer modifications than in plasma. We infer from this example that our method can be used to identify and characterize distinct proteoforms and, optionally, enrich them, thereby yielding the characteristics of proteoform-selective biomarkers.
Collapse
Affiliation(s)
- Heidrun Rhode
- Institute of Biochemistry I, Nonnenplan 2-4, University Hospital Jena, 07740, Jena, Germany.
| | - Petra Muckova
- Institute of Biochemistry I, Nonnenplan 2-4, University Hospital Jena, 07740, Jena, Germany
| | - Rita Büchler
- Institute of Biochemistry I, Nonnenplan 2-4, University Hospital Jena, 07740, Jena, Germany.,Pharmachem Straße 1, Pharmachem Pößneck GmbH & Co. KG, 07381, Pößneck, Germany
| | - Sindy Wendler
- Institute of Biochemistry I, Nonnenplan 2-4, University Hospital Jena, 07740, Jena, Germany.,Institute of Microbiology, Am Klinikum 1, University Hospital Jena, 07747, Jena, Germany
| | - Bärbel Tautkus
- Institute of Biochemistry I, Nonnenplan 2-4, University Hospital Jena, 07740, Jena, Germany
| | - Michaela Vogel
- Institute of Biochemistry I, Nonnenplan 2-4, University Hospital Jena, 07740, Jena, Germany
| | - Thomas Moore
- Analytik Jena, Konrad-Zuse-Str.1, 07745, Jena, Germany
| | - Julian Grosskreutz
- Department of Neurology, Am Klinikum 1, University Hospital Jena, 07747, Jena, Germany
| | - Andree Klemm
- KfH Kuratorium für Dialyse und Nierentransplantation e.V., Ernst-Ruska-Ring 19, 07745, Jena, Germany
| | - Mary Nabity
- Department of Veterinary Pathobiology, College of Veterinary Medicine, 4467 TAMU, Texas A&M University, College Station, TX, 77843-4467, Texas, USA
| |
Collapse
|
2
|
Han S, Yang K, Zhu H, Liu J, Zhang L, Zhao J. Proteomics investigation of the changes in serum proteins after high- and low-flux hemodialysis. Ren Fail 2018; 40:506-513. [PMID: 30284957 PMCID: PMC6179064 DOI: 10.1080/0886022x.2018.1491406] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 06/10/2018] [Accepted: 06/14/2018] [Indexed: 01/09/2023] Open
Abstract
PURPOSE This study aimed to use proteomics methods to investigate the changes in serum protein levels after high- and low-flux hemodialysis (HD). METHODS Before and after HD, serum samples were obtained from two selected patients who were treated with a Polyflux 140 H high-flux dialyzer and a Polyflux 14 L low-flux dialyzer during two continuous therapy sessions. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) was performed to identify the proteins. RESULTS A total of 212 and 203 serum proteins were identified after high-flux and low-flux HD, respectively. After high-flux HD, 21 proteins increased, and 132 proteins decreased. After low-flux HD, 87 proteins increased, and 45 proteins decreased. High-flux HD led to a significantly greater reduction in protein levels than low-flux HD (0.73 ± 0.13 vs. 0.84 ± 0.18, p = .00). Among the increased and decreased proteins, the isoelectric point (pI) values mainly ranged from 5 to 7, and the molecular weights (Mws) were mostly smaller than 30 kDa. The serum proteins showed no difference in pI or Mw for high- and low-flux HD. Gene ontology (GO) analysis showed that the detected proteins were related to immune system processes and complement activation. CONCLUSIONS Serum protein levels differentially changed after high- and low-flux HD. Long-term effects should be observed in future studies.
Collapse
Affiliation(s)
- Shuai Han
- Affiliated Zhongshan Hospital of Dalian University, Dalian, China
| | - Kaiguang Yang
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, National Chromatographic Research and Analysis Center, Dalian, China
| | - Hong Zhu
- Affiliated Zhongshan Hospital of Dalian University, Dalian, China
| | - Jianhui Liu
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, National Chromatographic Research and Analysis Center, Dalian, China
| | - Lihua Zhang
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, National Chromatographic Research and Analysis Center, Dalian, China
| | - Jiuyang Zhao
- Department of Nephritic Medicine, Second Affiliated Hospital of Dalian Medical University, Dalian, China
| |
Collapse
|
3
|
Schrödl W, Büchler R, Wendler S, Reinhold P, Muckova P, Reindl J, Rhode H. Acute phase proteins as promising biomarkers: Perspectives and limitations for human and veterinary medicine. Proteomics Clin Appl 2016; 10:1077-1092. [PMID: 27274000 DOI: 10.1002/prca.201600028] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 05/09/2016] [Accepted: 06/01/2016] [Indexed: 12/23/2022]
Abstract
Acute phase proteins (APPs) are highly conserved plasma proteins that are increasingly secreted by the liver in response to a variety of injuries, independently of their location and cause. APPs favor the systemic regulation of defense, coagulation, proteolysis, and tissue repair. Various APPs have been applied as general diagnostic parameters for a long time. Through proteomic techniques, more and more APPs have been discovered to be differentially altered. Since they are not consistently explainable by a stereotypic hepatic expression of sets of APPs, most of these results have unfortunately been neglected or attributed to the nonspecificity of the acute phase reaction. Moreover, it appears that various extrahepatic tissues are also able to express APPs. These extrahepatic APPs show focally specific roles in tissue homeostasis and repair and are released primarily into interstitial and distal fluids. Since these focal proteins might leak into the circulatory system, mixtures of hepatic and extrahepatic APP species can be expected in blood. Hence, a selective alteration of parts of APPs might be expected. There are several hints on multiple molecular forms and fragments of tissue-derived APPs. These differences offer the chance for multiple selective determinations. Thus, specific proteoforms might indeed serve as tissue-specific disease indicators.
Collapse
Affiliation(s)
- Wieland Schrödl
- Institute of Bacteriology and Mycology, Veterinary Faculty, University Leipzig, Germany
| | - Rita Büchler
- Institute of Biochemistry I, University Hospital Jena, Germany
| | - Sindy Wendler
- Institute of Biochemistry I, University Hospital Jena, Germany
| | - Petra Reinhold
- Institute of Molecular Pathogenesis at 'Friedrich Loeffler Institut', Federal Research Institute for Animal Health, Jena, Germany
| | - Petra Muckova
- Institute of Biochemistry I, University Hospital Jena, Germany.,Clinic of Neurology, University Hospital Jena, Germany
| | - Johanna Reindl
- Institute of Biochemistry I, University Hospital Jena, Germany
| | - Heidrun Rhode
- Institute of Biochemistry I, University Hospital Jena, Germany
| |
Collapse
|
4
|
Mullen W, Saigusa D, Abe T, Adamski J, Mischak H. Proteomics and Metabolomics as Tools to Unravel Novel Culprits and Mechanisms of Uremic Toxicity: Instrument or Hype? Semin Nephrol 2014; 34:180-90. [DOI: 10.1016/j.semnephrol.2014.02.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
|
5
|
Speeckaert MM, Speeckaert R, van Geel N, Delanghe JR. Vitamin D binding protein: a multifunctional protein of clinical importance. Adv Clin Chem 2014; 63:1-57. [PMID: 24783350 DOI: 10.1016/b978-0-12-800094-6.00001-7] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Since the discovery of group-specific component and its polymorphism by Hirschfeld in 1959, research has put spotlight on this multifunctional transport protein (vitamin D binding protein, DBP). Besides the transport of vitamin D metabolites, DBP is a plasma glycoprotein with many important functions, including sequestration of actin, modulation of immune and inflammatory responses, binding of fatty acids, and control of bone development. A considerable DBP polymorphism has been described with a specific allele distribution in different geographic area. Multiple studies have shed light on the interesting relationship between polymorphisms of the DBP gene and the susceptibility to diseases. In this review, we give an overview of the multifunctional character of DBP and describe the clinical importance of DBP and its polymorphisms. Finally, we discuss the possibilities to use DBP as a novel therapeutic agent.
Collapse
|
6
|
Lin YP, Yang CY, Liao CC, Yu WC, Chi CW, Lin CH. Plasma protein characteristics of long-term hemodialysis survivors. PLoS One 2012; 7:e40232. [PMID: 22792249 PMCID: PMC3391220 DOI: 10.1371/journal.pone.0040232] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Accepted: 06/03/2012] [Indexed: 01/19/2023] Open
Abstract
Hemodialysis (HD) patients are under recurrent circulatory stress, and hemodialysis has a high mortality rate. The characteristics of plasma proteomes in patients surviving long-term HD remain obscure, as well as the potential biomarkers in predicting prognoses. This study reports the proteome analyses of patient plasma from non-diabetic long-term HD (LHD, dialysis vintage 14.9±4.1 years, n = 6) and the age/sex/uremic etiology-comparable short-term HD (SHD, dialysis vintage 5.3±2.9 years, n = 6) using 2-DE and mass spectrometry. In addition, a 4-year longitudinal follow-up of 60 non-diabetic HD patients was subsequently conducted to analyze the baseline plasma proteins by ELISA in predicting prognosis. Compared to the SHD, the LHD survivors had increased plasma vitamin D binding proteins (DBP) and decreased clusterin, apolipoprotein A-IV, haptoglobin, hemopexin, complement factors B and H, and altered isoforms of α1-antitrypsin and fibrinogen gamma. During the 45.7±15 months for follow-up of the 60 HD patient cases, 16 patients died. Kaplan-Meier analysis demonstrated that HD patients with the lowest tertile of the baseline plasma DBP level have a significantly higher mortality rate. Multivariate Cox regression analysis further indicated that DBP is an independent predictor of mortality. In summary, the altered plasma proteins in LHD implicated accelerated atherosclerosis, defective antioxidative activity, increased inflammation/infection, and organ dysfunction. Furthermore, lower baseline plasma DBP in HD patients is related to mortality. The results suggest that the proteomic approach could help discover the potential biomarker in HD prognoses.
Collapse
Affiliation(s)
- Yao-Ping Lin
- Institute of Clinical Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan
- Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Chih-Yu Yang
- Institute of Clinical Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan
- Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Chen-Chung Liao
- Proteomics Research Center, National Yang-Ming University, Taipei, Taiwan
| | - Wen-Chung Yu
- Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Chin-Wen Chi
- Department of Medical Research and Education, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Chao-Hsiung Lin
- Proteomics Research Center, National Yang-Ming University, Taipei, Taiwan
- Department of Medical Research and Education, Taipei Veterans General Hospital, Taipei, Taiwan
- Department of Life Sciences and Institute of Genomic Sciences, National Yang-Ming University, Taipei, Taiwan
- Department of Education and Research, Taipei City Hospital, Taipei, Taiwan
- * E-mail:
| |
Collapse
|
7
|
Walkowiak B, Sobol AB, Walczynska M, Kaminska M. Effect of uremia and hemodialysis on proteome profile of blood platelets and plasma. Clin Appl Thromb Hemost 2012; 19:541-9. [PMID: 22517926 DOI: 10.1177/1076029612444004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The aim of the present research was to assess the differences in blood platelet and plasma proteome profiles of patients with uremia in comparison with healthy participants. It was found that 23 peptides in the platelet proteome profiles of hemodialyzed patients and only 6 peptides in nondialyzed patients were upregulated. On the other hand, 18 peptides with reduced expression in nondialyzed patients and only 1 peptide in hemodialyzed patients were found. For serum, only 6 upregulated peptides in patients undergoing hemodialysis and 15 peptides in nondialyzed patients were found, most of these were about 10 kDa. A decrease in serum peptide expression was not observed. In conclusion, it should be noted that the process of hemodialysis modifies the platelet proteome to a greater extent than uremia alone, however the sera of nondialyzed patients have much larger amounts of low-molecular-weight peptides than those of hemodialyzed patients.
Collapse
Affiliation(s)
- Bogdan Walkowiak
- 1Department of Biophysics, Technical University of Lodz, Stefanowskiego, Lodz, Poland
| | | | | | | |
Collapse
|