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Vanarsa K, Zhang T, Hutcheson J, Kumar SR, Nukala S, Inthavong H, Stanley B, Wu T, Mok CC, Saxena R, Mohan C. iTRAQ-based mass spectrometry screen to identify serum biomarkers in systemic lupus erythematosus. Lupus Sci Med 2024; 11:e000673. [PMID: 38782493 PMCID: PMC11116855 DOI: 10.1136/lupus-2022-000673] [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] [Received: 02/02/2022] [Accepted: 09/15/2022] [Indexed: 05/25/2024]
Abstract
OBJECTIVE Systemic lupus erythematosus (SLE) is a complex systemic autoimmune disorder with no reliable serum biomarkers currently available other than autoantibodies. METHODS In the present study, isobaric tags for relative and absolute quantitation-based mass spectrometry was used to screen the sera of patients with SLE to uncover potential disease biomarkers. RESULTS 85 common proteins were identified, with 16 being elevated (≥1.3) and 23 being decreased (≤0.7) in SLE. Of the 16 elevated proteins, serum alpha-1-microglobulin/bikunin precursor (AMBP), zinc alpha-2 glycoprotein (AZGP) and retinol-binding protein 4 (RBP4) were validated in independent cross-sectional cohorts (Cohort I, N=52; Cohort II, N=117) using an orthogonal platform, ELISA. Serum AMBP, AZGP and RBP4 were validated to be significantly elevated in both patients with inactive SLE and patients with active SLE compared with healthy controls (HCs) (p<0.05, fold change >2.5) in Cohort I. All three proteins exhibited good discriminatory power for distinguishing active SLE and inactive SLE (area under the curve=0.82-0.96), from HCs. Serum AMBP exhibited the largest fold change in active SLE (5.96) compared with HCs and correlated with renal disease activity. The elevation in serum AMBP was validated in a second cohort of patients with SLE of different ethnic origins, correlating with serum creatinine (r=0.60, p<0.001). CONCLUSION Since serum AMBP is validated to be elevated in SLE and correlated with renal disease, the clinical utility of this novel biomarker warrants further analysis in longitudinal cohorts of patients with lupus and lupus nephritis.
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Affiliation(s)
- Kamala Vanarsa
- Department Biomedical Engineering, University of Houston, Houston, Texas, USA
| | - Ting Zhang
- University of Houston, Houston, Texas, USA
- Rheumatology, The Second Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | | | - Sneha Ravi Kumar
- Department Biomedical Engineering, University of Houston, Houston, Texas, USA
| | | | - Haleigh Inthavong
- Department Biomedical Engineering, University of Houston, Houston, Texas, USA
| | | | - Tianfu Wu
- Department Biomedical Engineering, University of Houston, Houston, Texas, USA
| | - C C Mok
- Medicine, Tuen Mun Hospital, Hong Kong
| | - Ramesh Saxena
- The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Chandra Mohan
- Department Biomedical Engineering, University of Houston, Houston, Texas, USA
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Li M, Zhong X, Feng Y, Li L. Novel Isobaric Tagging Reagent Enabled Multiplex Quantitative Glycoproteomics via Electron-Transfer/Higher-Energy Collisional Dissociation (EThcD) Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1874-1882. [PMID: 36095095 PMCID: PMC10160164 DOI: 10.1021/jasms.2c00177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Protein glycosylation, covalent attachment of carbohydrates to polypeptide chains, is a highly important post-translational modification involved in many essential physiological processes. Comprehensive site-specific and quantitative analysis is crucial for revealing the diverse functions and dynamics of glycosylation. To characterize intact glycopeptides, mass spectrometry (MS)-based glycoproteomics employs versatile fragmentation methods, among which electron-transfer/higher-energy collision dissociation (EThcD) has gained great popularity. However, the inherent limitation of EThcD in fragmenting low-charge ions has prevented its widespread applications. Furthermore, there is a need to develop a high-throughput strategy for comparative glycoproteomics with a large cohort of samples. Herein, we developed isobaric N,N-dimethyl leucine-derivatized ethylenediamine (DiLeuEN) tags to increase the charge states of glycopeptides, thereby improving the fragmentation efficiency and allowing for in-depth intact glycopeptide analysis, especially for sialoglycopeptides. Moreover, the unique reporter ions of DiLeuEN-labeled glycopeptides generated in tandem MS spectra enable relative quantification of up to four samples in a single analysis, which represents a new high-throughput method for quantitative glycoproteomics.
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Recent advances in proteomics and its implications in pituitary endocrine disorders. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2021; 1869:140700. [PMID: 34303023 DOI: 10.1016/j.bbapap.2021.140700] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 07/03/2021] [Accepted: 07/15/2021] [Indexed: 12/15/2022]
Abstract
Pituitary adenoma is considered as one of the most frequent intracranial tumors having salient impact on human health such as mass effects, hypopituitarism and visual defects etc. During the past few decades, there has been enormous advancement in mass spectrometry (MS)-based proteomics. However, very little is known about the molecular pathogenesis of pituitary adenomas in the context of proteomics. In this review article, we have focused on the provenance of pituitary tumors and their pathogenesis with the help of MS-based proteomics approaches. Recent advancements in quantitative proteomic approaches are outlined here that would be useful in the near pituitary adenoma proteomics research. This review discusses the enormous potential of pituitary adenomas research through proteomics with a common aim of deciphering disease pathobiology and identifying the work done in studying pituitary tumors during past decade.
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Su M, Zhang Z, Zhou L, Han C, Huang C, Nice EC. Proteomics, Personalized Medicine and Cancer. Cancers (Basel) 2021; 13:2512. [PMID: 34063807 PMCID: PMC8196570 DOI: 10.3390/cancers13112512] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 05/12/2021] [Accepted: 05/17/2021] [Indexed: 02/05/2023] Open
Abstract
As of 2020 the human genome and proteome are both at >90% completion based on high stringency analyses. This has been largely achieved by major technological advances over the last 20 years and has enlarged our understanding of human health and disease, including cancer, and is supporting the current trend towards personalized/precision medicine. This is due to improved screening, novel therapeutic approaches and an increased understanding of underlying cancer biology. However, cancer is a complex, heterogeneous disease modulated by genetic, molecular, cellular, tissue, population, environmental and socioeconomic factors, which evolve with time. In spite of recent advances in treatment that have resulted in improved patient outcomes, prognosis is still poor for many patients with certain cancers (e.g., mesothelioma, pancreatic and brain cancer) with a high death rate associated with late diagnosis. In this review we overview key hallmarks of cancer (e.g., autophagy, the role of redox signaling), current unmet clinical needs, the requirement for sensitive and specific biomarkers for early detection, surveillance, prognosis and drug monitoring, the role of the microbiome and the goals of personalized/precision medicine, discussing how emerging omics technologies can further inform on these areas. Exemplars from recent onco-proteogenomic-related publications will be given. Finally, we will address future perspectives, not only from the standpoint of perceived advances in treatment, but also from the hurdles that have to be overcome.
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Affiliation(s)
- Miao Su
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China; (M.S.); (Z.Z.); (L.Z.); (C.H.)
| | - Zhe Zhang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China; (M.S.); (Z.Z.); (L.Z.); (C.H.)
| | - Li Zhou
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China; (M.S.); (Z.Z.); (L.Z.); (C.H.)
| | - Chao Han
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China; (M.S.); (Z.Z.); (L.Z.); (C.H.)
| | - Canhua Huang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China; (M.S.); (Z.Z.); (L.Z.); (C.H.)
| | - Edouard C. Nice
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia
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Proteomic Studies of Psychiatric Disorders. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2019; 1735:59-89. [PMID: 29380307 DOI: 10.1007/978-1-4939-7614-0_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Many diseases result from programming effects in utero. This chapter describes recent advances in proteomic studies which have improved our understanding of the underlying pathophysiological pathways in the major psychiatric disorders, resulting in the development of potential novel biomarker tests. Such tests should be based on measurement of blood-based proteins given the ease of accessibility of this medium and the known connections between the periphery and the central nervous system. Most importantly, emerging biomarker tests should be developed on lab-on-a-chip and other handheld devices to enable point-of-care use. This should help to identify individuals with psychiatric disorders much sooner than ever before, which will allow more rapid treatment options for the best possible patient outcomes.
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Abstract
Peripheral blood mononuclear cells (PBMCs) have been used as a surrogate model of immune function in studies of multiple medical areas, such as metabolic diseases and immune dysfunction. This chapter describes a standardized technique for blood draw and preparation of PBMCs from whole blood using density gradient centrifugation, followed by cell culture. The main focus is on collection of the PBMC culture media and extraction of cellular proteins in order to provide the materials for biomarker studies.
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Affiliation(s)
- Hassan Rahmoune
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Paul C Guest
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil.
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Guest PC. Identification of Neural Stem Cell Biomarkers by Isobaric Tagging for Relative and Absolute Quantitation (iTRAQ) Mass Spectrometry. Methods Mol Biol 2018; 1735:467-476. [PMID: 29380337 DOI: 10.1007/978-1-4939-7614-0_34] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
This chapter describes a proteomic analysis of neural progenitor cells using isobaric tagging for relative and absolute quantitation (iTRAQ) mass spectrometry. A detailed procedure is described for the isolation, proliferation, and differentiation of these cells, including a comparative iTRAQ mass spectrometry analysis of the precursor and differentiated states. In total, there were changes in the levels of 55 proteins, many of which are not resolved easily by other proteomic methods. Therefore, this method should be useful for the identification of important regulatory molecules in the study of other precursor cells involved in neuronal or metabolic regulation in nutritional programming diseases.
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Affiliation(s)
- Paul C Guest
- Laboratory of Neuroproteomics, Institute of Biology, University of Campinas, Campinas, Brazil.
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Abstract
Cell adhesion to components of the cellular microenvironment via cell-surface adhesion receptors controls many aspects of cell behavior in a range of physiological and pathological processes. Multimolecular complexes of scaffolding and signaling proteins are recruited to the intracellular domains of adhesion receptors such as integrins, and these adhesion complexes tether the cytoskeleton to the plasma membrane and compartmentalize cellular signaling events. Integrin adhesion complexes are highly dynamic, and their assembly is tightly regulated. Comprehensive, unbiased, quantitative analyses of the composition of different adhesion complexes over the course of their formation will enable better understanding of how the dynamics of adhesion protein recruitment influence the functions of adhesion complexes in fundamental cellular processes. Here, a pipeline is detailed integrating biochemical isolation of integrin adhesion complexes during a time course, quantitative proteomic analysis of isolated adhesion complexes, and computational analysis of temporal proteomic data. This approach enables the characterization of adhesion complex composition and dynamics during complex assembly.
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Affiliation(s)
- Adam Byron
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK.
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Liu X, Dai R, Ke M, Suheryani I, Meng W, Deng Y. Differential Proteomic Analysis of Dimethylnitrosamine (DMN)-Induced Liver Fibrosis. Proteomics 2017; 17. [DOI: 10.1002/pmic.201700267] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 09/27/2017] [Indexed: 12/24/2022]
Affiliation(s)
- Xiujie Liu
- School of Life Science; Beijing Institute of Technology; Beijing P. R. China
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmceuticals; Beijing Institute of Technology; Beijing P. R. China
| | - Rongji Dai
- School of Life Science; Beijing Institute of Technology; Beijing P. R. China
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmceuticals; Beijing Institute of Technology; Beijing P. R. China
| | - Ming Ke
- School of Life Science; Beijing Institute of Technology; Beijing P. R. China
| | - Imran Suheryani
- School of Life Science; Beijing Institute of Technology; Beijing P. R. China
| | - Weiwei Meng
- School of Life Science; Beijing Institute of Technology; Beijing P. R. China
| | - Yulin Deng
- School of Life Science; Beijing Institute of Technology; Beijing P. R. China
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmceuticals; Beijing Institute of Technology; Beijing P. R. China
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