1
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Abdeen AH, Trist BG, Nikseresht S, Harwood R, Roudeau S, Rowlands BD, Kreilaus F, Cottam V, Mor D, Richardson M, Siciliano J, Forkgen J, Schaffer G, Genoud S, Li AA, Proschogo N, Antonio B, Falkenberg G, Brueckner D, Kysenius K, Liddell JR, Fat SCM, Wu S, Fifita J, Lockwood TE, Bishop DP, Blair I, Ortega R, Crouch PJ, Double KL. Parkinson-like wild-type superoxide dismutase 1 pathology induces nigral dopamine neuron degeneration in a novel murine model. Acta Neuropathol 2025; 149:22. [PMID: 40042537 PMCID: PMC11882636 DOI: 10.1007/s00401-025-02859-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2024] [Revised: 02/12/2025] [Accepted: 02/12/2025] [Indexed: 03/09/2025]
Abstract
Atypical wild-type superoxide dismutase 1 (SOD1) protein misfolding and deposition occurs specifically within the degenerating substantia nigra pars compacta (SNc) in Parkinson disease. Mechanisms driving the formation of this pathology and relationship with SNc dopamine neuron health are yet to be fully understood. We applied proteomic mass spectrometry and synchrotron-based biometal quantification to post-mortem brain tissues from the SNc of Parkinson disease patients and age-matched controls to uncover key factors underlying the formation of wild-type SOD1 pathology in this disorder. We also engineered two of these factors - brain copper deficiency and upregulated SOD1 protein levels - into a novel mouse strain, termed the SOCK mouse, to verify their involvement in the development of Parkinson-like wild-type SOD1 pathology and their impact on dopamine neuron health. Soluble SOD1 protein in the degenerating Parkinson disease SNc exhibited altered post-translational modifications, which may underlie changes to the enzymatic activity and aggregation of the protein in this region. These include decreased copper binding, dysregulation of physiological glycosylation, and atypical oxidation and glycation of key SOD1 amino acid residues. We demonstrated that the biochemical profile introduced in SOCK mice promotes the same post-translational modifications and the development of Parkinson-like wild-type SOD1 pathology in the midbrain and cortex. This pathology accumulates progressively with age and is accompanied by nigrostriatal degeneration and dysfunction, which occur in the absence of α-synuclein deposition. These mice do not exhibit weight loss nor spinal cord motor neuron degeneration, distinguishing them from transgenic mutant SOD1 mouse models. This study provides the first in vivo evidence that mismetallation and altered post-translational modifications precipitates wild-type SOD1 misfolding, dysfunction, and deposition in the Parkinson disease brain, which may contribute to SNc dopamine neuron degeneration. Our data position this pathology as a novel drug target for this disorder, with a particular focus on therapies capable of correcting alterations to SOD1 post-translational modifications.
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Affiliation(s)
- Amr H Abdeen
- Brain and Mind Centre and School of Medical Sciences (Neuroscience), Faculty of Medicine and Health, The University of Sydney, 94-100 Mallett Street, Camperdown, Sydney, NSW, 2006, Australia
| | - Benjamin G Trist
- Brain and Mind Centre and School of Medical Sciences (Neuroscience), Faculty of Medicine and Health, The University of Sydney, 94-100 Mallett Street, Camperdown, Sydney, NSW, 2006, Australia
| | - Sara Nikseresht
- Department of Anatomy & Physiology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, VIC, 3052, Australia
| | - Richard Harwood
- Sydney Microscopy and Microanalysis, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Stéphane Roudeau
- Univ. Bordeaux, CNRS, LP2I Bordeaux, UMR 5797, 33170, Gradignan, France
| | - Benjamin D Rowlands
- Brain and Mind Centre and School of Medical Sciences (Neuroscience), Faculty of Medicine and Health, The University of Sydney, 94-100 Mallett Street, Camperdown, Sydney, NSW, 2006, Australia
| | - Fabian Kreilaus
- Brain and Mind Centre and School of Medical Sciences (Neuroscience), Faculty of Medicine and Health, The University of Sydney, 94-100 Mallett Street, Camperdown, Sydney, NSW, 2006, Australia
| | - Veronica Cottam
- Brain and Mind Centre and School of Medical Sciences (Neuroscience), Faculty of Medicine and Health, The University of Sydney, 94-100 Mallett Street, Camperdown, Sydney, NSW, 2006, Australia
| | - David Mor
- Brain and Mind Centre and School of Medical Sciences (Neuroscience), Faculty of Medicine and Health, The University of Sydney, 94-100 Mallett Street, Camperdown, Sydney, NSW, 2006, Australia
| | - Miriam Richardson
- Brain and Mind Centre and School of Medical Sciences (Neuroscience), Faculty of Medicine and Health, The University of Sydney, 94-100 Mallett Street, Camperdown, Sydney, NSW, 2006, Australia
| | - Joel Siciliano
- Brain and Mind Centre and School of Medical Sciences (Neuroscience), Faculty of Medicine and Health, The University of Sydney, 94-100 Mallett Street, Camperdown, Sydney, NSW, 2006, Australia
| | - Julia Forkgen
- Brain and Mind Centre and School of Medical Sciences (Neuroscience), Faculty of Medicine and Health, The University of Sydney, 94-100 Mallett Street, Camperdown, Sydney, NSW, 2006, Australia
| | - Greta Schaffer
- Brain and Mind Centre and School of Medical Sciences (Neuroscience), Faculty of Medicine and Health, The University of Sydney, 94-100 Mallett Street, Camperdown, Sydney, NSW, 2006, Australia
| | - Sian Genoud
- Brain and Mind Centre and School of Medical Sciences (Neuroscience), Faculty of Medicine and Health, The University of Sydney, 94-100 Mallett Street, Camperdown, Sydney, NSW, 2006, Australia
| | - Anne A Li
- Brain and Mind Centre and School of Medical Sciences (Neuroscience), Faculty of Medicine and Health, The University of Sydney, 94-100 Mallett Street, Camperdown, Sydney, NSW, 2006, Australia
| | - Nicholas Proschogo
- Mass Spectrometry Facility, Faculty of Science, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Bernadeth Antonio
- Mass Spectrometry Facility, Faculty of Science, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Gerald Falkenberg
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Dennis Brueckner
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607, Hamburg, Germany
| | - Kai Kysenius
- Department of Anatomy & Physiology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, VIC, 3052, Australia
| | - Jeffrey R Liddell
- Department of Anatomy & Physiology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, VIC, 3052, Australia
| | - Sandrine Chan Moi Fat
- Motor Neuron Disease Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, Australia
| | - Sharlynn Wu
- Motor Neuron Disease Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, Australia
| | - Jennifer Fifita
- Motor Neuron Disease Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, Australia
| | - Thomas E Lockwood
- Hyphenated Mass Spectrometry Laboratory, Faculty of Science, University of Technology Sydney, Sydney, NSW, 2007, Australia
| | - David P Bishop
- Hyphenated Mass Spectrometry Laboratory, Faculty of Science, University of Technology Sydney, Sydney, NSW, 2007, Australia
| | - Ian Blair
- Motor Neuron Disease Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, Australia
| | - Richard Ortega
- Univ. Bordeaux, CNRS, LP2I Bordeaux, UMR 5797, 33170, Gradignan, France
| | - Peter J Crouch
- Department of Anatomy & Physiology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, VIC, 3052, Australia
| | - Kay L Double
- Brain and Mind Centre and School of Medical Sciences (Neuroscience), Faculty of Medicine and Health, The University of Sydney, 94-100 Mallett Street, Camperdown, Sydney, NSW, 2006, Australia.
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2
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She YM, Jia Z, Zhang X. Region-selective and site-specific glycation of influenza proteins surrounding the viral envelope membrane. Sci Rep 2024; 14:18975. [PMID: 39152175 PMCID: PMC11329638 DOI: 10.1038/s41598-024-69793-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Accepted: 08/08/2024] [Indexed: 08/19/2024] Open
Abstract
Analysis of protein modifications is critical for quality control of therapeutic biologics. However, the identification and quantification of naturally occurring glycation of membrane proteins by mass spectrometry remain technically challenging. We used highly sensitive LC MS/MS analyses combined with multiple enzyme digestions to determine low abundance early-stage lysine glycation products of influenza vaccines derived from embryonated chicken eggs and cultured cells. Straightforward sequencing was enhanced by MS/MS fragmentation of small peptides. As a result, we determined a widespread distribution of lysine modifications attributed by the region-selectivity and site-specificity of glycation toward influenza matrix 1, hemagglutinin and neuraminidase. Topological analysis provides insights into the site-specific lysine glycation, localizing in the distinct structural regions of proteins surrounding the viral envelope membrane. Our finding highlights the proteome-wide discovery of lysine glycation of influenza membrane proteins and potential effects on the structural assembly, stability, receptor binding and enzyme activity, demonstrating that the impacts of accumulated glycation on the quality of products can be directly monitored by mass spectrometry-based structural proteomics analyses.
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Affiliation(s)
- Yi-Min She
- Centre for Oncology, Radiopharmaceuticals and Research, Biologic and Radiopharmaceutical Drugs Directorate, Health Canada, Ottawa, ON, K1A 0K9, Canada.
| | - Zongchao Jia
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, K7L 3N6, Canada
| | - Xu Zhang
- Centre for Oncology, Radiopharmaceuticals and Research, Biologic and Radiopharmaceutical Drugs Directorate, Health Canada, Ottawa, ON, K1A 0K9, Canada.
- School of Pharmaceutical Sciences, Faculty of Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada.
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3
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Buchowiecka AK. Evidence of Gas Phase Glucosyl Transfer and Glycation in the CID/HCD-Spectra of S-Glucosylated Peptides. Int J Mol Sci 2024; 25:7483. [PMID: 39000590 PMCID: PMC11242366 DOI: 10.3390/ijms25137483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 06/30/2024] [Accepted: 07/02/2024] [Indexed: 07/16/2024] Open
Abstract
Protein cysteine S-glycosylation is a relatively rare and less well characterized post-translational modification (PTM). Creating reliable model proteins that carry this modification is challenging. The lack of available models or natural S-glycosylated proteins significantly hampers the development of mass-spectrometry-based (MS-based) methodologies for detecting protein cysteine S-glycosylation in real-world proteomic studies. There is also limited MS-sequencing data describing it as easier to create synthetic S-glycopeptides. Here, we present the results of an in-depth manual analysis of automatically annotated CID/HCD spectra for model S-glucopeptides. The CID spectra show a long series of y/b-fragment ions with retained S-glucosylation, regardless of the dominant m/z signals corresponding to neutral loss of 1,2-anhydroglucose from the precursor ions. In addition, the spectra show signals manifesting glucosyl transfer from the cysteine position onto lysine, arginine (Lys, Arg) side chains, and a peptide N-terminus. Other spectral evidence indicates that the N-glucosylated initial products of transfer are converted into N-fructosylated (i.e., glycated) structures due to Amadori rearrangement. We discuss the peculiar transfer of the glucose oxocarbenium ion (Glc+) to positively charged guanidinium residue (ArgH+) and propose a mechanism for the gas-phase Amadori rearrangement involving a 1,2-hydride ion shift.
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Affiliation(s)
- Alicja K Buchowiecka
- Institute of Molecular and Industrial Biotechnology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Stefanowskiego 2/22, 90-537 Łódź, Poland
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4
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Senavirathna L, Pan S, Chen R. Protein Advanced Glycation End Products and Their Implications in Pancreatic Cancer. Cancer Prev Res (Phila) 2023; 16:601-610. [PMID: 37578815 PMCID: PMC10843555 DOI: 10.1158/1940-6207.capr-23-0162] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 07/14/2023] [Accepted: 08/10/2023] [Indexed: 08/15/2023]
Abstract
Protein advanced glycation end products (AGE) formed by nonenzymatic glycation can disrupt the normal structure and function of proteins, and stimulate the receptor for AGEs (RAGE), triggering intricate mechanisms that are etiologically related to various chronic diseases, including pancreatic cancer. Many common risk factors of pancreatic cancer are the major sources for the formation of protein AGEs and glycative stress in the human body. Abnormal accumulation of protein AGEs can impair the cellular proteome and promote AGE-RAGE driven pro-inflammatory signaling cascades, leading to increased oxidative stress, protease resistance, protein dysregulation, transcription activity of STAT, NF-κB, and AP-1, aberrant status in ubiquitin-proteasome system and autophagy, as well as other molecular events that are susceptible for the carcinogenic transformation towards the development of neoplasms. Here, we review studies to highlight our understanding in the orchestrated molecular events in bridging the impaired proteome, dysregulated functional networks, and cancer hallmarks initiated upon protein AGE formation and accumulation in pancreatic cancer.
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Affiliation(s)
- Lakmini Senavirathna
- The Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Sheng Pan
- The Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- Department of Integrative Biology and Pharmacology, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Ru Chen
- Section of Gastroenterology and Hepatology, Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
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5
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Bader JM, Albrecht V, Mann M. MS-based proteomics of body fluids: The end of the beginning. Mol Cell Proteomics 2023:100577. [PMID: 37209816 PMCID: PMC10388585 DOI: 10.1016/j.mcpro.2023.100577] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 05/07/2023] [Accepted: 05/11/2023] [Indexed: 05/22/2023] Open
Abstract
Accurate biomarkers are a crucial and necessary precondition for precision medicine, yet existing ones are often unspecific and new ones have been very slow to enter the clinic. Mass spectrometry (MS)-based proteomics excels by its untargeted nature, specificity of identification and quantification making it an ideal technology for biomarker discovery and routine measurement. It has unique attributes compared to affinity binder technologies, such as OLINK Proximity Extension Assay and SOMAscan. In a previous review we described technological and conceptual limitations that had held back success (Geyer et al., 2017). We proposed a 'rectangular strategy' to better separate true biomarkers by minimizing cohort-specific effects. Today, this has converged with advances in MS-based proteomics technology, such as increased sample throughput, depth of identification and quantification. As a result, biomarker discovery studies have become more successful, producing biomarker candidates that withstand independent verification and, in some cases, already outperform state-of-the-art clinical assays. We summarize developments over the last years, including the benefits of large and independent cohorts, which are necessary for clinical acceptance. They are also required for machine learning or deep learning. Shorter gradients, new scan modes and multiplexing are about to drastically increase throughput, cross-study integration, and quantification, including proxies for absolute levels. We have found that multi-protein panels are inherently more robust than current single analyte tests and better capture the complexity of human phenotypes. Routine MS measurement in the clinic is fast becoming a viable option. The full set of proteins in a body fluid (global proteome) is the most important reference and the best process control. Additionally, it increasingly has all the information that could be obtained from targeted analysis although the latter may be the most straightforward way to enter into regular use. Many challenges remain, not least of a regulatory and ethical nature, but the outlook for MS-based clinical applications has never been brighter.
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Affiliation(s)
- Jakob M Bader
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Vincent Albrecht
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany; Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark.
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6
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Ma W, Ang IL, Lei KMK, Lam MMT, Zhang P, Poon TCW. Pitfalls and Solutions in Mass Spectrometry-Based Identification of Protein Glycation. Anal Chem 2023; 95:1829-1837. [PMID: 36630282 DOI: 10.1021/acs.analchem.2c01261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Emerging evidence suggests that advanced glycation end-products (AGEs) such as Nε-(carboxymethyl)lysine (CML) and Nε-(carboxymethyl)lysine (CEL) may play important roles in certain human diseases. Reliable analytical methods are needed for their characterizations and measurements. Pitfalls have been reported for applications of LC-MS/MS to identify various types of post-translational modifications, but not yet for the case of AGEs. Here, we showed that in the absence of manual inspection, cysteine alkylation with 2-iodoacetamide (IAA) can result in false-positive/ambiguous identifications of CML >20%. They were attributed to offsite alkylation together with incorrect monoisotopic peak assignment (pitfall 1) or together with deamidation (pitfall 2). For pitfall 1, false-positive identifications can be alleviated using a peptide mass error tolerance ≤5 ppm during the database search. Pitfall 2 results in ambiguous modification assignments, which may be overcome by using other alkylation reagents. According to calculations of theoretical mass shifts, the use of other common alkylation reagents (iodoacetic acid, 2-chloroacetamide, and acrylamide) should face similar pitfalls. The use of acrylamide can result in false-positive identifications of CEL instead of CML. Subsequently, we showed that compared to IAA, the use of N-isopropylacrylamide (NIPAM) as an alkylation reagent achieved similar levels of proteome coverage, while reducing the offsite alkylation reactions at lysine by more than five times. Furthermore, false-positive/ambiguous identifications of CML due to the two types of pitfalls were absent when using NIPAM. NIPAM alkylation results in a unique mass shift that allows reliable identifications of CML and most likely other AGEs, such as CEL.
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Affiliation(s)
- Wendong Ma
- Pilot Laboratory, MOE Frontier Science Centre for Precision Oncology, Centre for Precision Medicine Research and Training, Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macau 999078, China
| | - Irene Ling Ang
- Pilot Laboratory, MOE Frontier Science Centre for Precision Oncology, Centre for Precision Medicine Research and Training, Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macau 999078, China
| | - Kate M K Lei
- Pilot Laboratory, MOE Frontier Science Centre for Precision Oncology, Centre for Precision Medicine Research and Training, Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macau 999078, China
| | - Melody Man Ting Lam
- Proteomics Core, Faculty of Health Sciences, University of Macau, Macau 999078, China
| | - Pengwei Zhang
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510120, China
| | - Terence Chuen Wai Poon
- Pilot Laboratory, MOE Frontier Science Centre for Precision Oncology, Centre for Precision Medicine Research and Training, Institute of Translational Medicine, Faculty of Health Sciences, University of Macau, Macau 999078, China
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7
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Schmutzler S, Wölk M, Hoffmann R. Differentiation and Quantitation of Coeluting Isomeric Amadori and Heyns Peptides Using Sugar-Specific Fragment Ion Ratios. Anal Chem 2022; 94:7909-7917. [PMID: 35609340 DOI: 10.1021/acs.analchem.2c00681] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
d-glucose and d-fructose present in blood, tissues, and organs of all mammals can react with amino groups, leading to glucated (Amadori) and fructated (Heyns) products, i.e., proteins glycated at lysine residues. While typically present at low concentration in humans, metabolic diseases including diabetes elevate sugar levels, favoring glycation and consecutive reactions leading to advanced glycation end products (AGEs) linked to diabetic complications and cardiovascular diseases. Analytical methods able to differentiate and to individually quantify Amadori- and Heyns-modified proteins in complex sample mixtures, e.g., serum, are still very limited. Here, we show that the reported and supposedly specific neutral losses displayed in tandem mass spectra of Heyns peptides cannot be used for a reliable differentiation as they were also observed for Amadori peptides. However, the combination of several neutral loss signals in fragment ion ratios at both precursor and fragment ion signals allowed the differentiation and relative quantitation of coeluting isomeric Amadori and Heyns peptides at different concentrations and peptide ratios. This was also true for digested human plasma. Thus, the presented strategy allows the quantitation of Amadori and Heyns peptides in complex samples, especially by spiking isotope-labeled peptides. This will allow searching for glucated and fructated biomarkers in clinical samples.
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Affiliation(s)
- Sebastian Schmutzler
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Universität Leipzig, 04103 Leipzig, Germany.,Center for Biotechnology and Biomedicine, Universität Leipzig, Deutscher Platz 5, 04103 Leipzig, Germany
| | - Michele Wölk
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Universität Leipzig, 04103 Leipzig, Germany.,Center for Biotechnology and Biomedicine, Universität Leipzig, Deutscher Platz 5, 04103 Leipzig, Germany
| | - Ralf Hoffmann
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Universität Leipzig, 04103 Leipzig, Germany.,Center for Biotechnology and Biomedicine, Universität Leipzig, Deutscher Platz 5, 04103 Leipzig, Germany
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8
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Trist BG, Genoud S, Roudeau S, Rookyard A, Abdeen A, Cottam V, Hare DJ, White M, Altvater J, Fifita JA, Hogan A, Grima N, Blair IP, Kysenius K, Crouch PJ, Carmona A, Rufin Y, Claverol S, Van Malderen S, Falkenberg G, Paterson DJ, Smith B, Troakes C, Vance C, Shaw CE, Al-Sarraj S, Cordwell S, Halliday G, Ortega R, Double KL. Altered SOD1 maturation and post-translational modification in amyotrophic lateral sclerosis spinal cord. Brain 2022; 145:3108-3130. [PMID: 35512359 PMCID: PMC9473357 DOI: 10.1093/brain/awac165] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 03/29/2022] [Accepted: 04/14/2022] [Indexed: 11/13/2022] Open
Abstract
Aberrant self-assembly and toxicity of wild-type and mutant superoxide dismutase 1 (SOD1) has been widely examined in silico, in vitro, and in transgenic animal models of amyotrophic lateral sclerosis (ALS). Detailed examination of the protein in disease-affected tissues from ALS patients, however, remains scarce. We employed histological, biochemical and analytical techniques to profile alterations to SOD1 protein deposition, subcellular localization, maturation and post-translational modification in post-mortem spinal cord tissues from ALS cases and controls. Tissues were dissected into ventral and dorsal spinal cord grey matter to assess the specificity of alterations within regions of motor neuron degeneration. We provide evidence of the mislocalization and accumulation of structurally-disordered, immature SOD1 protein conformers in spinal cord motor neurons of SOD1-linked and non-SOD1-linked familial ALS cases, and sporadic ALS cases, compared with control motor neurons. These changes were collectively associated with instability and mismetallation of enzymatically-active SOD1 dimers, as well as alterations to SOD1 post-translational modifications and molecular chaperones governing SOD1 maturation. Atypical changes to SOD1 protein were largely restricted to regions of neurodegeneration in ALS cases, and clearly differentiated all forms of ALS from controls. Substantial heterogeneity in the presence of these changes was also observed between ALS cases. Our data demonstrates that varying forms of SOD1 proteinopathy are a common feature of all forms of ALS, and support the presence of one or more convergent biochemical pathways leading to SOD1 proteinopathy in ALS. The majority of these alterations are specific to regions of neurodegeneration, and may therefore constitute valid targets for therapeutic development.
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Affiliation(s)
- Benjamin G Trist
- Brain and Mind Centre and School of Medical Sciences (Neuroscience), Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
| | - Sian Genoud
- Brain and Mind Centre and School of Medical Sciences (Neuroscience), Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
| | - Stéphane Roudeau
- Univ. Bordeaux, CNRS, CENBG, UMR 5797, F-33170 Gradignan, France
| | - Alexander Rookyard
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, NSW 2006, Australia
| | - Amr Abdeen
- Brain and Mind Centre and School of Medical Sciences (Neuroscience), Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
| | - Veronica Cottam
- Brain and Mind Centre and School of Medical Sciences (Neuroscience), Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
| | - Dominic J Hare
- School of Biosciences, The University of Melbourne, Parkville, Victoria 3010, Australia.,Atomic Medicine Initiative, University of Technology Sydney, Broadway, New South Wales 2007, Australia
| | - Melanie White
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, NSW 2006, Australia
| | - Jens Altvater
- Sydney Mass Spectrometry, The University of Sydney, Sydney, NSW 2006, Australia
| | - Jennifer A Fifita
- Centre for Motor Neuron Disease Research, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Alison Hogan
- Centre for Motor Neuron Disease Research, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Natalie Grima
- Centre for Motor Neuron Disease Research, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Ian P Blair
- Centre for Motor Neuron Disease Research, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Kai Kysenius
- Department of Biochemistry and Pharmacology, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Peter J Crouch
- Department of Biochemistry and Pharmacology, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Asuncion Carmona
- Univ. Bordeaux, CNRS, CENBG, UMR 5797, F-33170 Gradignan, France
| | - Yann Rufin
- Plateforme Biochimie, University of Bordeaux, France
| | | | - Stijn Van Malderen
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Gerald Falkenberg
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - David J Paterson
- Australian Synchrotron, ANSTO, Clayton, Victoria 3168, Australia
| | - Bradley Smith
- Maurice Wohl Clinical Neuroscience Institute and the Institute of Psychiatry, Psychology and Neuroscience, King's College London, Camberwell, SE5 9RT, London, UK
| | - Claire Troakes
- UK Dementia Research Institute at King's College London, 5 Cutcombe Road, London, SE5 9RT, UK
| | - Caroline Vance
- Maurice Wohl Clinical Neuroscience Institute and the Institute of Psychiatry, Psychology and Neuroscience, King's College London, Camberwell, SE5 9RT, London, UK
| | - Christopher E Shaw
- UK Dementia Research Institute at King's College London, 5 Cutcombe Road, London, SE5 9RT, UK
| | - Safa Al-Sarraj
- London Neurodegenerative Diseases Brain Bank, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, SE5 8AF, London, UK
| | - Stuart Cordwell
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, NSW 2006, Australia
| | - Glenda Halliday
- Brain and Mind Centre and School of Medical Sciences (Neuroscience), Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
| | - Richard Ortega
- Univ. Bordeaux, CNRS, CENBG, UMR 5797, F-33170 Gradignan, France
| | - Kay L Double
- Brain and Mind Centre and School of Medical Sciences (Neuroscience), Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
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9
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Proteomic Analysis of Methylglyoxal Modifications Reveals Susceptibility of Glycolytic Enzymes to Dicarbonyl Stress. Int J Mol Sci 2022; 23:ijms23073689. [PMID: 35409048 PMCID: PMC8998448 DOI: 10.3390/ijms23073689] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 03/12/2022] [Accepted: 03/17/2022] [Indexed: 12/13/2022] Open
Abstract
Methylglyoxal (MGO) is a highly reactive cellular metabolite that glycates lysine and arginine residues to form post-translational modifications known as advanced glycation end products. Because of their low abundance and low stoichiometry, few studies have reported their occurrence and site-specific locations in proteins. Proteomic analysis of WIL2-NS B lymphoblastoid cells in the absence and presence of exogenous MGO was conducted to investigate the extent of MGO modifications. We found over 500 MGO modified proteins, revealing an over-representation of these modifications on many glycolytic enzymes, as well as ribosomal and spliceosome proteins. Moreover, MGO modifications were observed on the active site residues of glycolytic enzymes that could alter their activity. We similarly observed modification of glycolytic enzymes across several epithelial cell lines and peripheral blood lymphocytes, with modification of fructose bisphosphate aldolase being observed in all samples. These results indicate that glycolytic proteins could be particularly prone to the formation of MGO adducts.
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10
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Silva AM, Moniz T, de Castro B, Rangel M. Human transferrin: An inorganic biochemistry perspective. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2021.214186] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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11
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Di Fiore A, Supuran CT, Scaloni A, De Simone G. Human carbonic anhydrases and post-translational modifications: a hidden world possibly affecting protein properties and functions. J Enzyme Inhib Med Chem 2021; 35:1450-1461. [PMID: 32648529 PMCID: PMC7470082 DOI: 10.1080/14756366.2020.1781846] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Human carbonic anhydrases (CAs) have become a well-recognized target for the design of inhibitors and activators with biomedical applications. Accordingly, an enormous amount of literature is available on their biochemical, functional and structural aspects. Nevertheless post-translational modifications (PTMs) occurring on these enzymes and their functional implications have been poorly investigated so far. To fill this gap, in this review we have analysed all PTMs occurring on human CAs, as deriving from the search in dedicated databases, showing a widespread occurrence of modification events in this enzyme family. By combining these data with sequence alignments, inspection of 3 D structures and available literature, we have summarised the possible functional implications of these PTMs. Although in some cases a clear correlation between a specific PTM and the CA function has been highlighted, many modification events still deserve further dedicated studies.
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Affiliation(s)
- Anna Di Fiore
- Istituto di Biostrutture e Bioimmagini-National Research Council, Napoli, Italy
| | - Claudiu T Supuran
- NEUROFARBA Department, Pharmaceutical and Nutraceutical Section, University of Firenze, Sesto Fiorentino, Italy
| | - Andrea Scaloni
- Proteomics and Mass Spectrometry Laboratory, ISPAAM, National Research Council, Napoli, Italy
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12
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Geyer PE, Mann SP, Treit PV, Mann M. Plasma Proteomes Can Be Reidentifiable and Potentially Contain Personally Sensitive and Incidental Findings. Mol Cell Proteomics 2021; 20:100035. [PMID: 33444735 PMCID: PMC7950134 DOI: 10.1074/mcp.ra120.002359] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 12/02/2020] [Accepted: 12/14/2020] [Indexed: 12/12/2022] Open
Abstract
The goal of clinical proteomics is to identify, quantify, and characterize proteins in body fluids or tissue to assist diagnosis, prognosis, and treatment of patients. In this way, it is similar to more mature omics technologies, such as genomics, that are increasingly applied in biomedicine. We argue that, similar to those fields, proteomics also faces ethical issues related to the kinds of information that is inherently obtained through sample measurement, although their acquisition was not the primary purpose. Specifically, we demonstrate the potential to identify individuals both by their characteristic, individual-specific protein levels and by variant peptides reporting on coding single nucleotide polymorphisms. Furthermore, it is in the nature of blood plasma proteomics profiling that it broadly reports on the health status of an individual-beyond the disease under investigation. Finally, we show that private and potentially sensitive information, such as ethnicity and pregnancy status, can increasingly be derived from proteomics data. Although this is potentially valuable not only to the individual, but also for biomedical research, it raises ethical questions similar to the incidental findings obtained through other omics technologies. We here introduce the necessity of-and argue for the desirability for-ethical and human-rights-related issues to be discussed within the proteomics community. Those thoughts are more fully developed in our accompanying manuscript. Appreciation and discussion of ethical aspects of proteomic research will allow for deeper, better-informed, more diverse, and, most importantly, wiser guidelines for clinical proteomics.
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Affiliation(s)
- Philipp E Geyer
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany; Faculty of Health Sciences, NNF Center for Protein Research, University of Copenhagen, Copenhagen, Denmark; OmicEra Diagnostics GmbH, Planegg, Germany.
| | - Sebastian Porsdam Mann
- Department of Media, Cognition and Communication, University of Copenhagen, Copenhagen, Denmark; Uehiro Center for Practical Ethics, Oxford University, Oxford, UK
| | - Peter V Treit
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany; Faculty of Health Sciences, NNF Center for Protein Research, University of Copenhagen, Copenhagen, Denmark.
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13
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Li W, Lin L, Yan D, Jin Y, Xu Y, Li Y, Ma M, Wu Z. Application of a Pseudotargeted MS Method for the Quantification of Glycated Hemoglobin for the Improved Diagnosis of Diabetes Mellitus. Anal Chem 2020; 92:3237-3245. [PMID: 31961136 DOI: 10.1021/acs.analchem.9b05046] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Weifeng Li
- Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen 518020, China
- Integrated Chinese and Western Medicine Postdoctoral Research Station, Jinan University, Guangzhou 510632, China
| | - Lin Lin
- Sustech Core Research Facilities, Southern University of Science and Technology, Shenzhen 518055, China
| | - Dewen Yan
- Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen 518020, China
| | - Yu Jin
- Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen 518020, China
| | - Yun Xu
- Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen 518020, China
| | - Yinghong Li
- Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen 518020, China
| | - Min Ma
- Integrated Chinese and Western Medicine Postdoctoral Research Station, Jinan University, Guangzhou 510632, China
| | - Zhengzhi Wu
- Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen 518020, China
- Integrated Chinese and Western Medicine Postdoctoral Research Station, Jinan University, Guangzhou 510632, China
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14
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Zhang L, Zhang Q. Glycated Plasma Proteins as More Sensitive Markers for Glycemic Control in Type 1 Diabetes. Proteomics Clin Appl 2020; 14:e1900104. [PMID: 31868294 DOI: 10.1002/prca.201900104] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 11/08/2019] [Indexed: 12/12/2022]
Abstract
PURPOSE Glycated hemoglobin (HbA1c) is used clinically for diagnosis and therapeutic management of diabetes. However, HbA1c reflects average blood glucose level over a long period. The aim of this study is to look for short period, more sensitive protein markers that correlate better with glycemic level. EXPERIMENTAL DESIGN The glycated proteome of human plasma from type 1 diabetic individuals with good and poor (n = 20 each) glycemic control are analyzed using an online two-dimensional proteomics approach. Selected glycated peptides are further validated for their potential as candidate biomarkers using parallel reaction monitoring. RESULTS 305 glycated peptides are quantified and 290 are significantly increased in samples with poor glycemic control. 76 of the 88 selected glycated peptides have receiver operating characteristic area under curve (AUC) values greater than 0.8. Six validated glycated peptides with high AUC show high correlation with HbA1c and have higher fold changes between poor and good glycemic control than HbA1c. The parent proteins have half-lives shorter than HbA1c. CONCLUSIONS AND CLINICAL RELEVANCE Using an advanced proteomics platform for protein glycation analysis, glycated peptides and proteins are identified that are promising as more sensitive, shorter term indicators of glycemic control in diabetic patients than the commonly used HbA1c.
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Affiliation(s)
- Lina Zhang
- Center for Translational Biomedical Research, University of North Carolina at Greensboro, North Carolina Research Campus, Kannapolis, NC, 28081, USA.,State Key Laboratory of Food Science & Technology, Jiangnan University, Wuxi, 214122, Jiangsu Province, China
| | - Qibin Zhang
- Center for Translational Biomedical Research, University of North Carolina at Greensboro, North Carolina Research Campus, Kannapolis, NC, 28081, USA.,Department of Chemistry & Biochemistry, University of North Carolina at Greensboro, Greensboro, NC, 27412, USA
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15
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Sun F, Suttapitugsakul S, Xiao H, Wu R. Comprehensive Analysis of Protein Glycation Reveals Its Potential Impacts on Protein Degradation and Gene Expression in Human Cells. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:2480-2490. [PMID: 31073893 PMCID: PMC6842084 DOI: 10.1007/s13361-019-02197-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Revised: 03/11/2019] [Accepted: 03/12/2019] [Indexed: 05/02/2023]
Abstract
Glycation as a type of non-enzymatic protein modification is related to aging and chronic diseases, especially diabetes. Global analysis of protein glycation will aid in a better understanding of its formation mechanism and biological significance. In this work, we comprehensively investigated protein glycation in human cells (HEK293T, Jurkat, and MCF7 cells). The current results indicated that this non-enzymatic modification was not random, and protein at the extracellular regions and the nucleus were more frequently glycated. Systematic and site-specific analysis of glycated proteins allowed us to study the effect of the primary sequences and secondary structures of proteins on glycation. Furthermore, nearly every enzyme in the glycolytic pathway was found to be glycated and a possible mechanism was proposed. Many glycation sites were also previously reported as acetylation and ubiquitination sites, which strongly suggested that this non-enzymatic modification may disturb protein degradation and gene expression. The current results will facilitate further studies of protein glycation in biomedical and clinical research.
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Affiliation(s)
- Fangxu Sun
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Suttipong Suttapitugsakul
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Haopeng Xiao
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Ronghu Wu
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
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16
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LI WF, YAN DW, JIN Y, LI HY, MA M, WU ZZ. Application of Mass Spectrometry in Analysis of Non-Enzymatic Glycation Proteins in Diabetic Blood. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2019. [DOI: 10.1016/s1872-2040(19)61197-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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17
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Wewer Albrechtsen NJ, Geyer PE, Doll S, Treit PV, Bojsen-Møller KN, Martinussen C, Jørgensen NB, Torekov SS, Meier F, Niu L, Santos A, Keilhauer EC, Holst JJ, Madsbad S, Mann M. Plasma Proteome Profiling Reveals Dynamics of Inflammatory and Lipid Homeostasis Markers after Roux-En-Y Gastric Bypass Surgery. Cell Syst 2018; 7:601-612.e3. [DOI: 10.1016/j.cels.2018.10.012] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 09/10/2018] [Accepted: 10/25/2018] [Indexed: 12/16/2022]
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18
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Jagadeeshaprasad M, Venkatasubramani V, Unnikrishnan AG, Kulkarni MJ. Albumin Abundance and Its Glycation Status Determine Hemoglobin Glycation. ACS OMEGA 2018; 3:12999-13008. [PMID: 30411025 PMCID: PMC6217588 DOI: 10.1021/acsomega.8b01702] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 09/24/2018] [Indexed: 05/17/2023]
Abstract
Diabetes diagnosis and management majorly depend upon the measurement of glycated hemoglobin (HbA1c) levels. Various factors influence HbA1c levels such as the use of various analytical methods and the presence of various clinical conditions. Plasma albumin levels were known to be negatively associated with HbA1c. However, the precise mechanism by which they affect HbA1c is not well understood. Therefore, we have studied the influence of albumin levels and its glycation status on hemoglobin glycation using erythrocyte culture experiments. Erythrocytes maintained at low albumin concentration exhibited relatively increased albumin and hemoglobin glycation as compared to that in those maintained at higher albumin concentration. Increase in albumin glycation may decrease its ability to protect hemoglobin glycation. This was demonstrated by treatment of erythrocytes with N(ε)-(carboxymethyl)lysine-modified serum albumin (CMSA), which failed to protect hemoglobin glycation; instead, it increased hemoglobin glycation. The inability of CMSA to reduce hemoglobin glycation was due to the lack of free lysine residues of albumin, which was corroborated by using N(ε)-(acetyl)lysine serum albumin (AcSA) and clinical diabetic plasma. This is the first study which demonstrates that the modification of lysine residues of albumin impairs its ability to inhibit hemoglobin glycation. Furthermore, correlation studies between HbA1c and albumin levels or relative albumin fructosamine from clinical subjects supported our experimental finding that albumin abundance and its glycation status influence hemoglobin glycation. Therefore, we propose albumin level and its glycation status to be quantified in conjunction with HbA1c for better management of diabetes.
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Affiliation(s)
| | - Vinashya Venkatasubramani
- Proteomics
Facility, Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune 411008, India
| | - Ambika G. Unnikrishnan
- Department
of Diabetes and Endocrine Research, Chellaram
Diabetes Institute, Pune 411021, Maharashtra, India
| | - Mahesh J. Kulkarni
- Proteomics
Facility, Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune 411008, India
- E-mail: . Tel: +91 20 25902541. Fax: +91 20 25902648
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19
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Gianazza E, Banfi C. Post-translational quantitation by SRM/MRM: applications in cardiology. Expert Rev Proteomics 2018; 15:477-502. [DOI: 10.1080/14789450.2018.1484283] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Erica Gianazza
- Unit of Proteomics, Centro Cardiologico Monzino IRCCS, Milan, Italy
| | - Cristina Banfi
- Unit of Proteomics, Centro Cardiologico Monzino IRCCS, Milan, Italy
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20
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Silva AMN, Coimbra JTS, Castro MM, Oliveira Â, Brás NF, Fernandes PA, Ramos MJ, Rangel M. Determining the glycation site specificity of human holo-transferrin. J Inorg Biochem 2018; 186:95-102. [PMID: 29860209 DOI: 10.1016/j.jinorgbio.2018.05.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 05/15/2018] [Accepted: 05/25/2018] [Indexed: 11/29/2022]
Abstract
Understanding the effect of glycation on the function of transferrin, the systemic iron transporter, is fundamental to fully grasp the mechanisms leading to the loss of iron homeostasis observed in diabetes mellitus (DM). The spontaneous reaction with protein amino groups is one of the main causes of glucose toxicity, but the site specificity of this reaction is still poorly understood. Here in, an in vitro approach was used to study human holo-transferrin glycation in detail. Lysine residues 103, 312 and 380 proved to be the most reactive sites, and overall glycation specificity was found to be remarkably different from that described for apo-transferrin. A computational biochemistry approach was subsequently applied to rationalize lysine reactivity. Even though pKa values, solvent accessible surface area, hydrogen bonds or the presence of nearby charged/polar residues could be related to lysine reactivity, these parameters do not suffice to describe glycation site specificity in holo-transferrin. Furthermore, analysis of the most reactive residues suggests that the correct lysine side chain orientation may play a fundamental role in reactivity. Nevertheless, in holo-transferrin, glycation occurs away from the iron-binding sites and, despite the observed iron release, the modification of apo-transferrin should play a more relevant role for the loss of iron-binding capacity observed in the blood serum of DM patients.
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Affiliation(s)
- André M N Silva
- REQUIMTE-LAQV, Dep. de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal.
| | - João T S Coimbra
- REQUIMTE-UCIBIO, Dep. de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - Maria M Castro
- REQUIMTE-LAQV, Dep. de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - Ângela Oliveira
- REQUIMTE-LAQV, Dep. de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - Natércia F Brás
- REQUIMTE-UCIBIO, Dep. de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - Pedro A Fernandes
- REQUIMTE-UCIBIO, Dep. de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - Maria J Ramos
- REQUIMTE-UCIBIO, Dep. de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - Maria Rangel
- REQUIMTE-LAQV, Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Rua de Jorge Viterbo Ferreira n228, 4050-313 Porto, Portugal
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21
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Abstract
Glycated proteins are emerging as good indicators for diabetes and age related diseases. However, the platform for analysis of glycated proteome has been relatively less well established. We here introduce an online 2D-LC-HCD-MS/MS platform for comprehensive glycated peptide quantification. This platform includes a boronate affinity column in the first dimension for enrichment, reversed phase nanoLC column in the second dimension for separation, a benchtop Orbitrap mass spectrometer with HCD-MS/MS for peptide sequencing, and MaxQuant bioinformatics tool for identification and quantification of glycated peptides. This online 2D-LC-HCD-MS/MS platform has high enrichment efficiency with 85% of identified peptides in the enriched fraction as glycated, high sensitivity for detection of glycated peptides with LOD and LOQ at 1.2 and 2.4 pg, respectively, and high reproducibility with interday CVs < 20% for 80% of the glycated peptides. The number of glycated peptides quantified in in vitro glycated human plasma increased more than 3-fold using this platform in comparison to that obtained using 1D-LC-HCD-MS/MS platform without boronate affinity enrichment. Application of this online platform to human plasma identified 376 glycated peptides from 10 μg of protein digests. This highly sensitive and reproducible online 2D platform is promising for glycated protein analysis of complex clinical samples.
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Affiliation(s)
- Lina Zhang
- Center for Translational Biomedical Research, University of North Carolina at Greensboro , North Carolina Research Campus, Kannapolis, North Carolina 28081, United States
| | - Chih-Wei Liu
- Center for Translational Biomedical Research, University of North Carolina at Greensboro , North Carolina Research Campus, Kannapolis, North Carolina 28081, United States
| | - Qibin Zhang
- Center for Translational Biomedical Research, University of North Carolina at Greensboro , North Carolina Research Campus, Kannapolis, North Carolina 28081, United States.,Department of Chemistry & Biochemistry, University of North Carolina at Greensboro , Greensboro, North Carolina 27412, United States
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22
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Soboleva A, Schmidt R, Vikhnina M, Grishina T, Frolov A. Maillard Proteomics: Opening New Pages. Int J Mol Sci 2017; 18:E2677. [PMID: 29231845 PMCID: PMC5751279 DOI: 10.3390/ijms18122677] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 11/29/2017] [Accepted: 12/05/2017] [Indexed: 12/12/2022] Open
Abstract
Protein glycation is a ubiquitous non-enzymatic post-translational modification, formed by reaction of protein amino and guanidino groups with carbonyl compounds, presumably reducing sugars and α-dicarbonyls. Resulting advanced glycation end products (AGEs) represent a highly heterogeneous group of compounds, deleterious in mammals due to their pro-inflammatory effect, and impact in pathogenesis of diabetes mellitus, Alzheimer's disease and ageing. The body of information on the mechanisms and pathways of AGE formation, acquired during the last decades, clearly indicates a certain site-specificity of glycation. It makes characterization of individual glycation sites a critical pre-requisite for understanding in vivo mechanisms of AGE formation and developing adequate nutritional and therapeutic approaches to reduce it in humans. In this context, proteomics is the methodology of choice to address site-specific molecular changes related to protein glycation. Therefore, here we summarize the methods of Maillard proteomics, specifically focusing on the techniques providing comprehensive structural and quantitative characterization of glycated proteome. Further, we address the novel break-through areas, recently established in the field of Maillard research, i.e., in vitro models based on synthetic peptides, site-based diagnostics of metabolism-related diseases (e.g., diabetes mellitus), proteomics of anti-glycative defense, and dynamics of plant glycated proteome during ageing and response to environmental stress.
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Affiliation(s)
- Alena Soboleva
- Department of Biochemistry, St. Petersburg State University, Saint Petersburg 199034, Russia.
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, 06120 Halle, Germany.
| | - Rico Schmidt
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin-Luther Universität Halle-Wittenberg, 06108 Halle, Germany.
| | - Maria Vikhnina
- Department of Biochemistry, St. Petersburg State University, Saint Petersburg 199034, Russia.
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, 06120 Halle, Germany.
| | - Tatiana Grishina
- Department of Biochemistry, St. Petersburg State University, Saint Petersburg 199034, Russia.
| | - Andrej Frolov
- Department of Biochemistry, St. Petersburg State University, Saint Petersburg 199034, Russia.
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, 06120 Halle, Germany.
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23
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Golizeh M, Lee K, Ilchenko S, Ösme A, Bena J, Sadygov RG, Kashyap SR, Kasumov T. Increased serotransferrin and ceruloplasmin turnover in diet-controlled patients with type 2 diabetes. Free Radic Biol Med 2017; 113:461-469. [PMID: 29079528 PMCID: PMC5739305 DOI: 10.1016/j.freeradbiomed.2017.10.373] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 09/22/2017] [Accepted: 10/22/2017] [Indexed: 01/07/2023]
Abstract
Type 2 diabetes mellitus (T2DM) is associated with oxidative stress and perturbed iron metabolism. Serotransferrin (Trf) and ceruloplasmin (Cp) are two key proteins involved in iron metabolism and anti-oxidant defense. Non-enzymatic glycation and oxidative modification of plasma proteins are known to occur under hyperglycemia and oxidative stress. In this study, shotgun proteomics and 2H2O-based metabolic labeling were used to characterize post-translational modifications and assess the kinetics of Trf and Cp in T2DM patients and matched controls in vivo. Six early lysine (Amadori) and one advanced arginine glycation were detected in Trf. No glycation, but five asparagine deamidations, were found in Cp. T2DM patients had increased fractional catabolic rates of both Trf and Cp that correlated with HbA1c (p < 0.05). The glycated Trf population was subject to an even faster degradation compared to the total Trf pool, suggesting that hyperglycemia contributed to an increased Trf degradation in T2DM patients. Enhanced production of Trf and Cp kept their levels stable. The changes in Trf and Cp turnover were associated with increased systemic oxidative stress without any alteration in iron status in T2DM. These findings can help better understand the potential role of altered Trf and Cp metabolism in the pathogenesis of T2DM and other diseases.
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Affiliation(s)
- Makan Golizeh
- Department of Pharmaceutical Sciences, Northeast Ohio Medical University, Rootstown, OH, United States
| | - Kwangwon Lee
- Department of Pharmaceutical Sciences, Northeast Ohio Medical University, Rootstown, OH, United States
| | - Serguei Ilchenko
- Department of Pharmaceutical Sciences, Northeast Ohio Medical University, Rootstown, OH, United States
| | - Abdullah Ösme
- Department of Pharmaceutical Sciences, Northeast Ohio Medical University, Rootstown, OH, United States
| | - James Bena
- Section of Biostatistics, Quantitative Health Sciences, Cleveland Clinic, Cleveland, OH, United States
| | - Rovshan G Sadygov
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, United States
| | - Sangeeta R Kashyap
- Department of Endocrinology, Cleveland Clinic, Cleveland, OH, United States
| | - Takhar Kasumov
- Department of Pharmaceutical Sciences, Northeast Ohio Medical University, Rootstown, OH, United States; Department of Endocrinology, Cleveland Clinic, Cleveland, OH, United States.
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