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Bhardwaj S, Bulluss M, D'Aubeterre A, Derakhshani A, Penner R, Mahajan M, Mahajan VB, Dufour A. Integrating the analysis of human biopsies using post-translational modifications proteomics. Protein Sci 2024; 33:e4979. [PMID: 38533548 DOI: 10.1002/pro.4979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 03/07/2024] [Accepted: 03/16/2024] [Indexed: 03/28/2024]
Abstract
Proteome diversities and their biological functions are significantly amplified by post-translational modifications (PTMs) of proteins. Shotgun proteomics, which does not typically survey PTMs, provides an incomplete picture of the complexity of human biopsies in health and disease. Recent advances in mass spectrometry-based proteomic techniques that enrich and study PTMs are helping to uncover molecular detail from the cellular level to system-wide functions, including how the microbiome impacts human diseases. Protein heterogeneity and disease complexity are challenging factors that make it difficult to characterize and treat disease. The search for clinical biomarkers to characterize disease mechanisms and complexity related to patient diagnoses and treatment has proven challenging. Knowledge of PTMs is fundamentally lacking. Characterization of complex human samples that clarify the role of PTMs and the microbiome in human diseases will result in new discoveries. This review highlights the key role of proteomic techniques used to characterize unknown biological functions of PTMs derived from complex human biopsies. Through the integration of diverse methods used to profile PTMs, this review explores the genetic regulation of proteoforms, cells of origin expressing specific proteins, and several bioactive PTMs and their subsequent analyses by liquid chromatography and tandem mass spectrometry.
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Affiliation(s)
- Sonali Bhardwaj
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- McCaig Institute for Bone and Joint Health, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Mitchell Bulluss
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- McCaig Institute for Bone and Joint Health, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Ana D'Aubeterre
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- McCaig Institute for Bone and Joint Health, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Afshin Derakhshani
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- McCaig Institute for Bone and Joint Health, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Regan Penner
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- McCaig Institute for Bone and Joint Health, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - MaryAnn Mahajan
- Molecular Surgery Laboratory, Stanford University, Palo Alto, California, USA
| | - Vinit B Mahajan
- Molecular Surgery Laboratory, Stanford University, Palo Alto, California, USA
- Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, California, USA
| | - Antoine Dufour
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- McCaig Institute for Bone and Joint Health, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
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Peng Y, Wang C, Ma W, Chen Q, Xu G, Kong Y, Ma L, Ding W, Zhang W. Deficiency of polypeptide N-acetylgalactosamine transferase 9 contributes to a risk for Parkinson's disease via mitochondrial dysfunctions. Int J Biol Macromol 2024; 263:130347. [PMID: 38401583 DOI: 10.1016/j.ijbiomac.2024.130347] [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: 09/14/2023] [Revised: 02/13/2024] [Accepted: 02/19/2024] [Indexed: 02/26/2024]
Abstract
Polypeptide N-acetylgalactosamine transferase 9 (GALNT9) catalyzes the initial step of mucin-type O-glycosylation via linking N-acetylgalactosamine (GalNAc) to serine/threonine in a protein. To unravel the association of GALNT9 with Parkinson's disease (PD), a progressive neurodegenerative disorder, GALNT9 levels were evaluated in the patients with PD and mice treated with 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine, and statistically analyzed based on the GEO datasets of GSE114918 and GSE216281. Glycoproteins with exposing GalNAc were purified using lectin affinity chromatography and identified by LC-MS/MS. The influence of GALNT9 on cells was evaluated via introducing a GALNT9-specific siRNA into SH-SY5Y cells. Consequently, GALNT9 deficiency was found to occur under PD conditions. GALNT9 silencing contributed to a causative factor in PD pathogenesis via reducing the levels of intracellular dopamine, tyrosine hydroxylase and soluble α-synuclein, and promoting α-synuclein aggregates. MS identification revealed 14 glycoproteins. 5 glycoproteins, including ACO2, ATP5B, CKB, CKMT1A, ALDOC, were associated with energy metabolism. GALNT9 silencing resulted in mitochondrial dysfunctions via increasing ROS accumulation, mitochondrial membrane depolarization, mPTPs opening, Ca2+ releasing and activation of the CytC-related apoptotic pathway. The dysfunctional mitochondria then triggered mitophagy, possibly intermediated by adenine nucleotide translocase 1. Our study suggests that GALNT9 is potentially developed into an auxiliary diagnostic index and therapeutic target of PD.
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Affiliation(s)
- Yuanwen Peng
- Department of Epidemiology, Dalian Medical University, Dalian 116044, China
| | - Cui Wang
- Department of Neurology, Dalian Municipal Central Hospital, Dalian 116033, China
| | - Wei Ma
- Biochemistry and Molecular Biology Department of College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, China
| | - Qianhui Chen
- Biochemistry and Molecular Biology Department of College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, China
| | - Guannan Xu
- Department of Epidemiology, Dalian Medical University, Dalian 116044, China
| | - Ying Kong
- Biochemistry and Molecular Biology Department of College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, China
| | - Li Ma
- Department of Epidemiology, Dalian Medical University, Dalian 116044, China
| | - Wenyong Ding
- Biochemistry and Molecular Biology Department of College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, China.
| | - Wenli Zhang
- Biochemistry and Molecular Biology Department of College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, China.
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Loh SN, Anthony IR, Gavor E, Lim XS, Kini RM, Mok YK, Sivaraman J. Recognition of Aedes aegypti Mosquito Saliva Protein LTRIN by the Human Receptor LTβR for Controlling the Immune Response. BIOLOGY 2024; 13:42. [PMID: 38248473 PMCID: PMC10813304 DOI: 10.3390/biology13010042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 01/04/2024] [Accepted: 01/08/2024] [Indexed: 01/23/2024]
Abstract
Salivary proteins from mosquitoes have received significant attention lately due to their potential to develop therapeutic treatments or vaccines for mosquito-borne diseases. Here, we report the characterization of LTRIN (lymphotoxin beta receptor inhibitor), a salivary protein known to enhance the pathogenicity of ZIKV by interrupting the LTβR-initiated NF-κB signaling pathway and, therefore, diminish the immune responses. We demonstrated that the truncated C-terminal LTRIN (ΔLTRIN) is a dimeric protein with a stable alpha helix-dominant secondary structure, which possibly aids in withstanding the temperature fluctuations during blood-feeding events. ΔLTRIN possesses two Ca2+ binding EF-hand domains, with the second EF-hand motif playing a more significant role in interacting with LTβR. Additionally, we mapped the primary binding regions of ΔLTRIN on LTβR using hydrogen-deuterium exchange mass spectrometry (HDX-MS) and identified that 91QEKAHIAEHMDVPIDTSKMSEQELQFHY118 from the N-terminal of ΔLTRIN is the major interacting region. Together, our studies provide insight into the recognition of LTRIN by LTβR. This finding may aid in a future therapeutic and transmission-blocking vaccine development against ZIKV.
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Affiliation(s)
- Su Ning Loh
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore; (S.N.L.)
| | - Ian Russell Anthony
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore; (S.N.L.)
| | - Edem Gavor
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore; (S.N.L.)
| | - Xin Shan Lim
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore; (S.N.L.)
| | - R. Manjunatha Kini
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore; (S.N.L.)
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117600, Singapore
| | - Yu Keung Mok
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore; (S.N.L.)
| | - J. Sivaraman
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore; (S.N.L.)
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Kobeissy F, Goli M, Yadikar H, Shakkour Z, Kurup M, Haidar MA, Alroumi S, Mondello S, Wang KK, Mechref Y. Advances in neuroproteomics for neurotrauma: unraveling insights for personalized medicine and future prospects. Front Neurol 2023; 14:1288740. [PMID: 38073638 PMCID: PMC10703396 DOI: 10.3389/fneur.2023.1288740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 11/01/2023] [Indexed: 02/12/2024] Open
Abstract
Neuroproteomics, an emerging field at the intersection of neuroscience and proteomics, has garnered significant attention in the context of neurotrauma research. Neuroproteomics involves the quantitative and qualitative analysis of nervous system components, essential for understanding the dynamic events involved in the vast areas of neuroscience, including, but not limited to, neuropsychiatric disorders, neurodegenerative disorders, mental illness, traumatic brain injury, chronic traumatic encephalopathy, and other neurodegenerative diseases. With advancements in mass spectrometry coupled with bioinformatics and systems biology, neuroproteomics has led to the development of innovative techniques such as microproteomics, single-cell proteomics, and imaging mass spectrometry, which have significantly impacted neuronal biomarker research. By analyzing the complex protein interactions and alterations that occur in the injured brain, neuroproteomics provides valuable insights into the pathophysiological mechanisms underlying neurotrauma. This review explores how such insights can be harnessed to advance personalized medicine (PM) approaches, tailoring treatments based on individual patient profiles. Additionally, we highlight the potential future prospects of neuroproteomics, such as identifying novel biomarkers and developing targeted therapies by employing artificial intelligence (AI) and machine learning (ML). By shedding light on neurotrauma's current state and future directions, this review aims to stimulate further research and collaboration in this promising and transformative field.
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Affiliation(s)
- Firas Kobeissy
- Department of Neurobiology, School of Medicine, Neuroscience Institute, Atlanta, GA, United States
| | - Mona Goli
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, United States
| | - Hamad Yadikar
- Department of Biological Sciences Faculty of Science, Kuwait University, Safat, Kuwait
| | - Zaynab Shakkour
- Department of Pathology and Anatomical Sciences, University of Missouri School of Medicine, Columbia, MO, United States
| | - Milin Kurup
- Alabama College of Osteopathic Medicine, Dothan, AL, United States
| | | | - Shahad Alroumi
- Department of Biological Sciences Faculty of Science, Kuwait University, Safat, Kuwait
| | - Stefania Mondello
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Messina, Italy
| | - Kevin K. Wang
- Department of Neurobiology, School of Medicine, Neuroscience Institute, Atlanta, GA, United States
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, United States
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Jiang P, Peng W, Zhao J, Goli M, Huang Y, Li Y, Mechref Y. Glycan/Protein-Stable Isotope Labeling in Cell Culture for Enabling Concurrent Quantitative Glycomics/Proteomics/Glycoproteomics. Anal Chem 2023; 95:16059-16069. [PMID: 37843510 DOI: 10.1021/acs.analchem.3c00247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2023]
Abstract
The complexity and heterogeneity of protein glycosylation present an analytical challenge to the studies of characterization and quantitation. Various LC-MS-based quantitation strategies have emerged in recent decades. Metabolic stable isotope labeling has been developed to enhance the accurate LC/MS-based quantitation between different cell lines. Stable isotope labeling by amino acids in a cell culture (SILAC) is the most widely used metabolic labeling method in proteomic analysis. However, it can only label the peptide backbone and is thus limited in glycomic studies. Here, we present a metabolic isotope labeling strategy, named GlyProSILC (Glycan Protein Stable Isotope Labeling in Cell Culture), that can label both the glycan motif and peptide backbone from the same batch of cells. It was performed by feeding cells with a heavy medium containing amide-15N-glutamine, 13C6-arginine (Arg6), and 13C6-15N2-lysine (Lys8). No significant change of cell line metabolism after GlyProSILC labeling was observed based on transcriptomic, glycomic, and proteomic data. The labeling conditions, labeling efficiency, and quantitation accuracy were investigated. After quantitation correction, we simultaneously quantified 62 N-glycans, 574 proteins, and 344 glycopeptides using the same batch of mixed 231BR/231 cell lines. So far, GlyProSILC provides an accurate and effective quantitation approach for glycomics, proteomics, and glycoproteomics in a cell culture system.
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Affiliation(s)
- Peilin Jiang
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Wenjing Peng
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Jingfu Zhao
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Mona Goli
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Yifan Huang
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Yunxiang Li
- Division of Chemistry and Biochemistry, Texas Woman's University, Denton, Texas 76204, United States
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
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Xue Q, Yang Y, Li H, Li X, Zou L, Li T, Ma H, Qi H, Wang J, Yu T. Functions and mechanisms of protein lysine butyrylation (Kbu): Therapeutic implications in human diseases. Genes Dis 2023; 10:2479-2490. [PMID: 37554202 PMCID: PMC10404885 DOI: 10.1016/j.gendis.2022.10.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 09/27/2022] [Accepted: 10/20/2022] [Indexed: 11/30/2022] Open
Abstract
Post-translational modifications (PTM) are covalent modifications of proteins or peptides caused by proteolytic cleavage or the attachment of moieties to one or more amino acids. PTMs play essential roles in biological function and regulation and have been linked with several diseases. Modifications of protein acylation (Kac), a type of PTM, are known to induce epigenetic regulatory processes that promote various diseases. Thus, an increasing number of studies focusing on acylation modifications are being undertaken. Butyrylation (Kbu) is a new acylation process found in animals and plants. Kbu has been recently linked to the onset and progression of several diseases, such as cancer, cardiovascular diseases, diabetes, and vascular dementia. Moreover, the mode of action of certain drugs used in the treatment of lymphoma and colon cancer is based on the regulation of butyrylation levels, suggesting that butyrylation may play a therapeutic role in these diseases. In addition, butyrylation is also commonly involved in rice gene expression and thus plays an important role in the growth, development, and metabolism of rice. The tools and analytical methods that could be utilized for the prediction and detection of lysine butyrylation have also been investigated. This study reviews the potential role of histone Kbu, as well as the mechanisms underlying this process. It also summarizes various enzymes and analytical methods associated with Kbu, with the goal of providing new insights into the role of Kbu in gene regulation and diseases.
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Affiliation(s)
- Qianqian Xue
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266000, China
| | - Yanyan Yang
- Department of Immunology, School of Basic Medicine, Qingdao University, Qingdao, Shandong 266021, China
| | - Hong Li
- Clinical Laboratory, Central Laboratory. The Affiliated Qingdao Hiser Hospital of Qingdao University, Qingdao, Shandong 266000, China
| | - Xiaoxin Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266000, China
| | - Lu Zou
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266000, China
| | - Tianxiang Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266000, China
| | - Huibo Ma
- Department of Vascular Surgery, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266000, China
| | - Hongzhao Qi
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266000, China
| | - Jianxun Wang
- Department of Immunology, School of Basic Medicine, Qingdao University, Qingdao, Shandong 266021, China
| | - Tao Yu
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266000, China
- Department of Cardiac Ultrasound, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266000, China
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Yang J, Li H, Zhao Y. Dessert or Poison? The Roles of Glycosylation in Alzheimer's, Parkinson's, Huntington's Disease, and Amyotrophic Lateral Sclerosis. Chembiochem 2023; 24:e202300017. [PMID: 37440197 DOI: 10.1002/cbic.202300017] [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: 01/19/2023] [Revised: 04/27/2023] [Indexed: 07/14/2023]
Abstract
Ministry of Education and Key Laboratory of Neurons and glial cells of the central nervous system (CNS) are modified by glycosylation and rely on glycosylation to achieve normal neural function. Neurodegenerative disease is a common disease of the elderly, affecting their healthy life span and quality of life, and no effective treatment is currently available. Recent research implies that various glycosylation traits are altered during neurodegenerative diseases, suggesting a potential implication of glycosylation in disease pathology. Herein, we summarized the current knowledge about glycosylation associated with Alzheimer's disease (AD), Parkinson's disease (PD), Huntington's disease (HD), and Amyotrophic lateral sclerosis (ALS) pathogenesis, focusing on their promising functional avenues. Moreover, we collected research aimed at highlighting the need for such studies to provide a wealth of disease-related glycosylation information that will help us better understand the pathophysiological mechanisms and hopefully specific glycosylation information to provide further diagnostic and therapeutic directions for neurodegenerative diseases.
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Affiliation(s)
- Jiajun Yang
- Department of Biochemistry and Molecular Biology School of Basic Medical Science, Guizhou Medical University, Guiyang, 550004, China
- Key Laboratory of Endemic and Ethenic Diseases Medical Molecular Biology of Guizhou Province Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Hongmei Li
- Department of Biochemistry and Molecular Biology School of Basic Medical Science, Guizhou Medical University, Guiyang, 550004, China
- Key Laboratory of Endemic and Ethenic Diseases Medical Molecular Biology of Guizhou Province Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Yuhui Zhao
- Key Laboratory of Endemic and Ethenic Diseases Medical Molecular Biology of Guizhou Province Guizhou Medical University, Guiyang, 550004, Guizhou, China
- Guizhou Medical University, Guiyang, 550004, China
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Wang X, Yue L, Zhang F, Tang Z, Chen Z, Li Z. A novel strategy for quantification of α2,3- and α2,6-linked sialic acids in sialylated glycoproteins. Carbohydr Res 2023; 531:108892. [PMID: 37429229 DOI: 10.1016/j.carres.2023.108892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 06/24/2023] [Accepted: 06/28/2023] [Indexed: 07/12/2023]
Abstract
Sialic acid, a monosaccharide containing nine carbon atoms, is widely distributed in eukaryotic cells. The bound sialic acids are mainly present at the glycan ends of glycoconjugates via α2-3 or α2-6 glycosidic bonds, and alterations in their expression levels and linkage types are associated with the progress of many diseases and tumors. The present study provides a new strategy for quantification of α2,3- and α2,6-linked sialic acids in sialylated glycoproteins. In fact, quantification of α2,3-linked sialic acids were based on the difference of the bound sialic acids in the sample before and after treatment with α2-3 neuraminidase, whereas the α2,6-linked sialic acids were equal to the bound sialic acids in the α2-3 neuraminidase-treated sample. Subsequently, α2,3/6-linked sialic acids in salivary glycoproteins from healthy volunteers and diabetic patients were quantified in accordance with this method. This work provides an accurate method for the quantification of α2,3- and α2,6-linked sialic acids in the sialoglycoproteins, which is more instructive for understanding the biological roles of α2,3/6-linked sialic acid in sialoglycoproteins.
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Affiliation(s)
- Xilong Wang
- College of Life Sciences and Technology, Longdong University, Qingyang, Gansu, China; Gansu Key Laboratory of Protection and Utilization for Biological Resources and Ecological Restoration, Qingyang, Gansu, China.
| | - Lixin Yue
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Fan Zhang
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, Shaanxi, China
| | - Zhen Tang
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, Shaanxi, China
| | - Zhuo Chen
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, Shaanxi, China
| | - Zheng Li
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, Shaanxi, China
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Kvist M, Välimaa L, Harel A, Malmi S, Tuomisto A. Glycans as Potential Diagnostic Markers of Traumatic Brain Injury in Children. Diagnostics (Basel) 2023; 13:2181. [PMID: 37443575 DOI: 10.3390/diagnostics13132181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 06/19/2023] [Accepted: 06/22/2023] [Indexed: 07/15/2023] Open
Abstract
Diagnosing mild traumatic brain injury (TBI) in the acute setting is challenging due to the nonspecific and often transient or delayed symptoms. Further, the criteria for acute head imaging are frequently not fulfilled, which may lead to a missed diagnosis. A rapid test to diagnose TBI using body fluids would be highly useful. Urine and saliva samples were collected from 28 pediatric patients (mean [SD] age, eight years two months [four years three months]) with acute, clinically diagnosed mild TBI and 30 healthy volunteers at Satasairaala Hospital, Pori, Finland, over 11 months. The mean (SD) time from trauma to first sampling was 3 h 56 min (1 h 14 min). Samples were analyzed to determine the number of lectin-binding glycan molecules, indicating nerve tissue damage. The relative levels of several lectin-bound glycans were measured by fluorescence. Compared with healthy controls, the TBI group showed significant increases (p < 0.05, Wilcoxon rank-sum two-sided test) in nine glycans in the saliva, one glycan in the urine, and a significant decrease in seven glycans in the urine. These findings of potentially diagnostic glycans in body fluids after TBI warrant further research and may enable the development of a rapid body fluid-based point-of-care test to identify pediatric patients with TBI after a head injury.
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Affiliation(s)
| | | | | | - Sari Malmi
- Department of Pediatric Surgery, Satasairaala Hospital, 28500 Pori, Finland
| | - Aleksi Tuomisto
- Department of Pediatric Surgery, Satasairaala Hospital, 28500 Pori, Finland
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Xue X, Wu X, Liu L, Liu L, Zhu F. ERVW-1 Activates ATF6-Mediated Unfolded Protein Response by Decreasing GANAB in Recent-Onset Schizophrenia. Viruses 2023; 15:1298. [PMID: 37376599 DOI: 10.3390/v15061298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/27/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
Schizophrenia, a mental disorder, afflicts 1% of the worldwide population. The dysregulation of homeostasis in the endoplasmic reticulum (ER) has been implicated in schizophrenia. Moreover, recent studies indicate that ER stress and the unfolded protein response (UPR) are linked to this mental disorder. Our previous research has verified that endogenous retrovirus group W member 1 envelope (ERVW-1), a risk factor for schizophrenia, is elevated in individuals with schizophrenia. Nevertheless, no literature is available regarding the underlying relationship between ER stress and ERVW-1 in schizophrenia. The aim of our research was to investigate the molecular mechanism connecting ER stress and ERVW-1 in schizophrenia. Here, we employed Gene Differential Expression Analysis to predict differentially expressed genes (DEGs) in the human prefrontal cortex of schizophrenic patients and identified aberrant expression of UPR-related genes. Subsequent research indicated that the UPR gene called XBP1 had a positive correlation with ATF6, BCL-2, and ERVW-1 in individuals with schizophrenia using Spearman correlation analysis. Furthermore, results from the enzyme-linked immunosorbent assay (ELISA) suggested increased serum protein levels of ATF6 and XBP1 in schizophrenic patients compared with healthy controls, exhibiting a strong correlation with ERVW-1 using median analysis and Mann-Whitney U analysis. However, serum GANAB levels were decreased in schizophrenic patients compared with controls and showed a significant negative correlation with ERVW-1, ATF6, and XBP1 in schizophrenic patients. Interestingly, in vitro experiments verified that ERVW-1 indeed increased ATF6 and XBP1 expression while decreasing GANAB expression. Additionally, the confocal microscope experiment suggested that ERVW-1 could impact the shape of the ER, leading to ER stress. GANAB was found to participate in ER stress regulated by ERVW-1. In conclusion, ERVW-1 induced ER stress by suppressing GANAB expression, thereby upregulating the expression of ATF6 and XBP1 and ultimately contributing to the development of schizophrenia.
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Affiliation(s)
- Xing Xue
- State Key Laboratory of Virology, Department of Medical Microbiology, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Xiulin Wu
- State Key Laboratory of Virology, Department of Medical Microbiology, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Lijuan Liu
- State Key Laboratory of Virology, Department of Medical Microbiology, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China
- Hubei Province Key Laboratory of Allergy & Immunology, Wuhan University, Wuhan 430071, China
| | | | - Fan Zhu
- State Key Laboratory of Virology, Department of Medical Microbiology, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China
- Hubei Province Key Laboratory of Allergy & Immunology, Wuhan University, Wuhan 430071, China
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11
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Pradeep P, Kang H, Lee B. Glycosylation and behavioral symptoms in neurological disorders. Transl Psychiatry 2023; 13:154. [PMID: 37156804 PMCID: PMC10167254 DOI: 10.1038/s41398-023-02446-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 04/19/2023] [Accepted: 04/24/2023] [Indexed: 05/10/2023] Open
Abstract
Glycosylation, the addition of glycans or carbohydrates to proteins, lipids, or other glycans, is a complex post-translational modification that plays a crucial role in cellular function. It is estimated that at least half of all mammalian proteins undergo glycosylation, underscoring its importance in the functioning of cells. This is reflected in the fact that a significant portion of the human genome, around 2%, is devoted to encoding enzymes involved in glycosylation. Changes in glycosylation have been linked to various neurological disorders, including Alzheimer's disease, Parkinson's disease, autism spectrum disorder, and schizophrenia. Despite its widespread occurrence, the role of glycosylation in the central nervous system remains largely unknown, particularly with regard to its impact on behavioral abnormalities in brain diseases. This review focuses on examining the role of three types of glycosylation: N-glycosylation, O-glycosylation, and O-GlcNAcylation, in the manifestation of behavioral and neurological symptoms in neurodevelopmental, neurodegenerative, and neuropsychiatric disorders.
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Affiliation(s)
- Prajitha Pradeep
- Center for Cognition and Sociality, Institute for Basic Science, Daejeon, 34126, South Korea
- IBS School, University of Science and Technology (UST), Daejeon, 34113, South Korea
| | - Hyeyeon Kang
- Center for Cognition and Sociality, Institute for Basic Science, Daejeon, 34126, South Korea
- Department of Biomedical Engineering, College of Information and Biotechnology, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, South Korea
| | - Boyoung Lee
- Center for Cognition and Sociality, Institute for Basic Science, Daejeon, 34126, South Korea.
- IBS School, University of Science and Technology (UST), Daejeon, 34113, South Korea.
- Department of Biomedical Engineering, College of Information and Biotechnology, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, South Korea.
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12
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Delafield DG, Miles HN, Ricke WA, Li L. Higher Temperature Porous Graphitic Carbon Separations Differentially Impact Distinct Glycopeptide Classes. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:64-74. [PMID: 36450095 PMCID: PMC9812930 DOI: 10.1021/jasms.2c00249] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Mass spectrometry-based discovery glycoproteomics is highly dependent on the use of chromatography paradigms amenable to analyte retention and separation. When compared against established stationary phases such as reversed-phase and hydrophilic interaction liquid chromatography, reports utilizing porous graphitic carbon have detailed its numerous advantages. Recent efforts have highlighted the utility in porous graphitic carbon in high-throughput glycoproteomics, principally through enhanced profiling depth and liquid-phase resolution at higher column temperatures. However, increasing column temperature has been shown to impart disparaging effects in glycopeptide identification. Herein we further elucidate this trend, describing qualitative and semiquantitative effects of increased column temperature on glycopeptide identification rates, signal intensity, resolution, and spectral count linear response. Through analysis of enriched bovine and human glycopeptides, species with high mannose and sialylated glycans were shown to most significantly benefit and suffer from high column temperatures, respectively. These results provide insight as to how porous graphitic carbon separations may be appropriately leveraged for glycopeptide identification while raising concerns over quantitative and semiquantitative label-free comparisons as the temperature changes. RAW MS glycoproteomic data are available via ProteomeXchange with identifier PXD034354.
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Affiliation(s)
- Daniel G. Delafield
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706
| | - Hannah N. Miles
- Division of Pharmaceutical Sciences, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53075
| | - William A. Ricke
- Division of Pharmaceutical Sciences, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53075
- George M. O’Brien Urology Research Center of Excellence, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
- Department of Urology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706
- Division of Pharmaceutical Sciences, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53075
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13
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Mumtaz I, Ayaz MO, Khan MS, Manzoor U, Ganayee MA, Bhat AQ, Dar GH, Alghamdi BS, Hashem AM, Dar MJ, Ashraf GM, Maqbool T. Clinical relevance of biomarkers, new therapeutic approaches, and role of post-translational modifications in the pathogenesis of Alzheimer's disease. Front Aging Neurosci 2022; 14:977411. [PMID: 36158539 PMCID: PMC9490081 DOI: 10.3389/fnagi.2022.977411] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 08/18/2022] [Indexed: 12/14/2022] Open
Abstract
Alzheimer's disease (AD) is a neurodegenerative disorder that causes progressive loss of cognitive functions like thinking, memory, reasoning, behavioral abilities, and social skills thus affecting the ability of a person to perform normal daily functions independently. There is no definitive cure for this disease, and treatment options available for the management of the disease are not very effective as well. Based on histopathology, AD is characterized by the accumulation of insoluble deposits of amyloid beta (Aβ) plaques and neurofibrillary tangles (NFTs). Although several molecular events contribute to the formation of these insoluble deposits, the aberrant post-translational modifications (PTMs) of AD-related proteins (like APP, Aβ, tau, and BACE1) are also known to be involved in the onset and progression of this disease. However, early diagnosis of the disease as well as the development of effective therapeutic approaches is impeded by lack of proper clinical biomarkers. In this review, we summarized the current status and clinical relevance of biomarkers from cerebrospinal fluid (CSF), blood and extracellular vesicles involved in onset and progression of AD. Moreover, we highlight the effects of several PTMs on the AD-related proteins, and provide an insight how these modifications impact the structure and function of proteins leading to AD pathology. Finally, for disease-modifying therapeutics, novel approaches, and targets are discussed for the successful treatment and management of AD.
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Affiliation(s)
- Ibtisam Mumtaz
- Laboratory of Nanotherapeutics and Regenerative Medicine, Department of Nanotechnology, University of Kashmir, Srinagar, India
| | - Mir Owais Ayaz
- Laboratory of Cell and Molecular Biology, Department of Cancer Pharmacology, CSIR-Indian Institute of Integrative Medicine, Jammu, India
- Centre for Scientific and Innovative Research, Ghaziabad, Utter Pradesh, India
| | - Mohamad Sultan Khan
- Neurobiology and Molecular Chronobiology Laboratory, Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Umar Manzoor
- Laboratory of Immune and Inflammatory Disease, Jeju Research Institute of Pharmaceutical Sciences, Jeju National University, Jeju, South Korea
| | - Mohd Azhardin Ganayee
- Laboratory of Nanotherapeutics and Regenerative Medicine, Department of Nanotechnology, University of Kashmir, Srinagar, India
- Department of Chemistry, Indian Institute of Technology Madras, Chennai, India
| | - Aadil Qadir Bhat
- Laboratory of Cell and Molecular Biology, Department of Cancer Pharmacology, CSIR-Indian Institute of Integrative Medicine, Jammu, India
- Centre for Scientific and Innovative Research, Ghaziabad, Utter Pradesh, India
| | - Ghulam Hassan Dar
- Sri Pratap College, Cluster University Srinagar, Jammu and Kashmir, India
| | - Badrah S. Alghamdi
- Department of Physiology, Neuroscience Unit, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
- Pre-clinical Research Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Anwar M. Hashem
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mohd Jamal Dar
- Laboratory of Cell and Molecular Biology, Department of Cancer Pharmacology, CSIR-Indian Institute of Integrative Medicine, Jammu, India
- Centre for Scientific and Innovative Research, Ghaziabad, Utter Pradesh, India
| | - Gulam Md. Ashraf
- Pre-clinical Research Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Tariq Maqbool
- Laboratory of Nanotherapeutics and Regenerative Medicine, Department of Nanotechnology, University of Kashmir, Srinagar, India
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14
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Bazard P, Pineros J, Acosta AA, Thivierge M, Paganella LR, Zucker S, Mannering FL, Modukuri S, Zhu X, Frisina RD, Ding B. Post-Translational Modifications and Age-related Hearing Loss. Hear Res 2022; 426:108625. [DOI: 10.1016/j.heares.2022.108625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 08/21/2022] [Accepted: 09/23/2022] [Indexed: 11/04/2022]
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15
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Liu R, Xia S, Li H. Native top-down mass spectrometry for higher-order structural characterization of proteins and complexes. MASS SPECTROMETRY REVIEWS 2022:e21793. [PMID: 35757976 DOI: 10.1002/mas.21793] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/23/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
Progress in structural biology research has led to a high demand for powerful and yet complementary analytical tools for structural characterization of proteins and protein complexes. This demand has significantly increased interest in native mass spectrometry (nMS), particularly native top-down mass spectrometry (nTDMS) in the past decade. This review highlights recent advances in nTDMS for structural research of biological assemblies, with a particular focus on the extra multi-layers of information enabled by TDMS. We include a short introduction of sample preparation and ionization to nMS, tandem fragmentation techniques as well as mass analyzers and software/analysis pipelines used for nTDMS. We highlight unique structural information offered by nTDMS and examples of its broad range of applications in proteins, protein-ligand interactions (metal, cofactor/drug, DNA/RNA, and protein), therapeutic antibodies and antigen-antibody complexes, membrane proteins, macromolecular machineries (ribosome, nucleosome, proteosome, and viruses), to endogenous protein complexes. The challenges, potential, along with perspectives of nTDMS methods for the analysis of proteins and protein assemblies in recombinant and biological samples are discussed.
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Affiliation(s)
- Ruijie Liu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Shujun Xia
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Huilin Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
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16
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Antunes ASLM. Post-translational Modifications in Parkinson’s Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1382:85-94. [DOI: 10.1007/978-3-031-05460-0_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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17
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Dagra A, Barpujari A, Bauer SZ, Olowofela BO, Mohamed S, McGrath K, Robinson C, Robicsek S, Snyder A, Lucke-Wold B. Epigenetics of Neurotrauma. NEUROLOGY (CHICAGO, ILL.) 2022; 2:42-47. [PMID: 36507115 PMCID: PMC9732507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Epigenetic changes have been linked to a host of disease states. Besides the physiological function of epigenetic changes in regulating cellular function, recent data indicates that key changes in epigenetic activity also play an important pathophysiologic role following neurotrauma specifically. Such manifestations occur through the activation or silencing of different genes. Histone methylation has emerged as a critical component of this process and can be selectively modulated after injury. Pre-clinical studies have resulted in key discoveries regarding specific methylation sites of interest. This focused review highlights some of these early findings and their relationship to clinical outcomes. These findings suggest areas of future investigation and discovery in the quest to develop ideal biomarkers and methods to utilize them in developing therapeutic interventions.
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Affiliation(s)
- A Dagra
- College of Medicine, University of Florida, USA
| | - A Barpujari
- College of Liberal Arts and Sciences, University of Florida, USA
| | - SZ Bauer
- College of Medicine, University of Nevada, USA
| | | | - S Mohamed
- College of Medicine, University of Florida, USA
| | - K McGrath
- College of Medicine, University of Florida, USA
| | - C Robinson
- Departments of Neurology and Neuroscience, McKnight Brain Institute, University of Florida, USA
- Department of Neuroscience, Center for Translational Research in Neurodegenerative Disease, and Brain Injury Rehabilitation and Neuroresilience Center, University of Florida, USA
| | - S Robicsek
- Department of Anesthesiology, University of Florida, USA
| | - A Snyder
- Department of Neuropsychology, University of Florida, USA
| | - B Lucke-Wold
- Department of Neurosurgery, University of Florida, USA
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18
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Lybech LKM, Calabró M, Briuglia S, Drago A, Crisafulli C. Suicide Related Phenotypes in a Bipolar Sample: Genetic Underpinnings. Genes (Basel) 2021; 12:genes12101482. [PMID: 34680877 PMCID: PMC8535342 DOI: 10.3390/genes12101482] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/20/2021] [Accepted: 09/21/2021] [Indexed: 12/31/2022] Open
Abstract
Suicide in Bipolar Disorder (BD) is a relevant clinical concern. Genetics may shape the individual risk for suicide behavior in BD, together with known clinical factors. The lack of consistent replication in BD may be associated with its multigenetic component. In the present contribution we analyzed a sample of BD individuals (from STEP-BD database) to identify the genetic variants potentially associated with three different suicide-related phenotypes: (1) a feeling that the life was not worth living; (2) fantasies about committing a violent suicide; (3) previous attempted suicide. The sample under analysis included 1115 BD individuals. None of the SNPs reached genome-wide significance. However, a trend of association was evidenced for rs2767403, an intron variant of AOPEP gene, in association with phenotype #1 (p = 5.977 × 10−6). The molecular pathway analysis showed a significant enrichment in all the investigated phenotypes on pathways related to post synaptic signaling, neurotransmission and neurodevelopment. Further, NOTCH signaling or the γ-aminobutyric acid (GABA)-ergic signaling were found to be associated with specific suicide-related phenotypes. The present investigation contributes to the hypothesis that the genetic architecture of suicide behaviors in BD is related to alteration of entire pathways rather than single genes. In particular, our molecular pathway analysis points on some specific molecular events that could be the focus of further research in this field.
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Affiliation(s)
- Line K. M. Lybech
- Unit for Psychiatric Research, Psychiatry, Aalborg University Hospital, DK-9100 Aalborg, Denmark;
| | - Marco Calabró
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, 98125 Messina, Italy; (M.C.); (S.B.)
| | - Silvana Briuglia
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, 98125 Messina, Italy; (M.C.); (S.B.)
| | - Antonio Drago
- Unit for Psychiatric Research, Psychiatry, Aalborg University Hospital, DK-9100 Aalborg, Denmark;
- Correspondence: (A.D.); (C.C.); Tel.: +45-97-64-30-00 (A.D.); +39-(0)9-0221-3373 (C.C.)
| | - Concetta Crisafulli
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, 98125 Messina, Italy; (M.C.); (S.B.)
- Correspondence: (A.D.); (C.C.); Tel.: +45-97-64-30-00 (A.D.); +39-(0)9-0221-3373 (C.C.)
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19
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Pedragosa J, Mercurio D, Oggioni M, Marquez-Kisinousky L, de Simoni MG, Planas AM. Mannose-binding lectin promotes blood-brain barrier breakdown and exacerbates axonal damage after traumatic brain injury in mice. Exp Neurol 2021; 346:113865. [PMID: 34547288 DOI: 10.1016/j.expneurol.2021.113865] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 08/19/2021] [Accepted: 09/14/2021] [Indexed: 12/23/2022]
Abstract
Leukocyte infiltration and blood-brain barrier breakdown contribute to secondary brain damage after traumatic brain injury (TBI). TBI induces neuroimmune responses triggering pathogenic complement activation through different pathways, including the lectin pathway. We investigated mechanisms underlying mannose-binding lectin (MBL)-mediated brain damage focusing on neutrophil infiltration and blood-brain barrier breakdown in a TBI mouse model. Wild type mice and MBL-/- null mice were subjected to controlled cortical impact. We studied neutrophil infiltration and regional localization by confocal microscopy 1, 4 and 15 days post-trauma, and investigated neutrophil extracellular trap (NET) formation. By immunofluorescence and/or Western blotting in various brain regions we studied the presence of fibrin(ogen), pentraxin-3, albumin and immunoglobulin G. Finally, we studied neurofilament proteins, synaptophysin, and αII-spectrin, and assessed white matter content in the injured tissue. TBI triggered an acute wave of neutrophil infiltration at day 1 followed by a more discrete persistence of neutrophils in the injured tissue at least until day 15. We detected the presence of NETs and pentraxin-3 in the injured tissue, as well as accumulation of fibrin(ogen), increased blood-brain barrier permeability, and neurofilament, synaptophysin and white matter loss, and calpain-mediated αII spectrin breakdown. MBL-/- mice showed reduced number of Ly6G+ neutrophils 4 days after TBI, lower accumulation of pentraxin-3 and fibrin(ogen) in the injured tissue, reduced global plasma protein extravasation, and better preservation of axonal and white matter integrity. These results show that MBL participates in secondary neutrophil accumulation and blood-brain barrier breakdown, and promotes axonal and white matter damage after TBI in mice.
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Affiliation(s)
- Jordi Pedragosa
- Department of Neuroscience and Experimental Therapeutics, Institute for Biomedical Research of Barcelona (IIBB), Spanish National Research Council (CSIC), Barcelona, Spain; Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Domenico Mercurio
- Department of Neuroscience, Istituto di Ricerche Farmacologiche Mario Negri-IRCCS, 20156 Milan, Italy
| | - Marco Oggioni
- Department of Neuroscience, Istituto di Ricerche Farmacologiche Mario Negri-IRCCS, 20156 Milan, Italy
| | - Leonardo Marquez-Kisinousky
- Department of Neuroscience and Experimental Therapeutics, Institute for Biomedical Research of Barcelona (IIBB), Spanish National Research Council (CSIC), Barcelona, Spain; Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Maria-Grazia de Simoni
- Department of Neuroscience, Istituto di Ricerche Farmacologiche Mario Negri-IRCCS, 20156 Milan, Italy
| | - Anna M Planas
- Department of Neuroscience and Experimental Therapeutics, Institute for Biomedical Research of Barcelona (IIBB), Spanish National Research Council (CSIC), Barcelona, Spain; Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.
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20
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SHANG S, DONG H, LI Y, ZHANG W, LI H, QIN W, QIAN X. [Large-scale enrichment and identification of human urinary N-glycoproteins/ N-glycopeptides]. Se Pu 2021; 39:686-694. [PMID: 34227365 PMCID: PMC9421575 DOI: 10.3724/sp.j.1123.2021.01039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Indexed: 11/25/2022] Open
Abstract
N-Glycosylation of proteins, an important post-translational modification in eukaryotic cells, plays an essential role in the regulation of cell adhesion, migration, signal transduction, and apoptosis. Abnormal changes in protein glycosylation are closely related to the occurrence of many critical diseases, including diabetes, tumors, and neurological, kidney, and inflammatory diseases. A non-invasive type of liquid biopsy, urine sampling has the advantage of reducing the complexity of proteomic analysis. This facilitates the design of large-scale and continuous or multi-time point sampling strategies. However, the dynamic range of urinary protein abundance is relatively large, owing to individual differences and physiological conditions. Currently, there is a lack of specialized research on individual differences, physiological fluctuations, and physiological abundance ranges of urinary N-glycoproteins in large healthy populations. Therefore, it is difficult to accurately distinguish individual differences and normal physiological fluctuations from changes caused by disease; this poses a great challenge in disease marker research. Liquid chromatography-mass spectrometry (LC-MS) is an analytical technique widely used for the large-scale profiling of proteomes in biological systems, and the enrichment of N-glycopeptides is a prerequisite for their detection by MS.In this study, we established an approach based on hydrophilic interaction chromatography (HILIC) by optimizing the activation, cleaning, and elution processes of the enrichment method, for instance through the optimization of particle size and solvent composition, and investigated the identification number, selectivity, and stability of N-glycoprotein/N-glycopeptide enrichment under different experimental conditions. We found that N-glycoproteins and N-glycopeptides were highly enriched in a trifluoroacetic acid system with 5-μm filling particles in the HILIC column. On this basis, we analyzed the levels of N-glycoproteins/N-glycopeptides in urine samples. The consistency of N-glycoprotein/N-glycopeptide levels in urine samples taken from the same healthy person for five consecutive days was investigated by correlation analysis. This analysis revealed that the urinary N-glycoproteome of the same healthy person was relatively stable over a short period of time. Next, urinary samples from 20 healthy male volunteers and 20 healthy female volunteers were enriched for N-glycoproteins/N-glycopeptides, which were profiled by MS through qualitative and quantitative analyses. Screening and functional analysis of differential proteins were then carried out. A total of 1016 N-glycoproteins and 2192 N-glycopeptides were identified in the mid-morning urine samples of the 40 healthy volunteers. A label-free quantitation strategy was used to investigate the fluctuation range of the physiologically abundant urinary N-glycopeptides. The abundance of urinary N-glycopeptides spanned across approximately five orders of magnitude. Subsequently, gender differences in the N-glycosylation levels of urinary proteins were also explored in healthy people. Functional analysis of the N-glycoproteins that exhibited gender differences in abundance was performed. Based on multivariate statistical analysis, 206 differentially expressed proteins (p<0.05, fold change (FC)> 4) were identified. In females, we found 175 significantly down-regulated N-glycoproteins and 31 significantly up-regulated N-glycoproteins with respect to males. The expression levels of N-glycopeptides between the two groups suggested a clear gender difference. To investigate the biological processes and functions of these proteins, gene ontology (GO) analysis was performed on the N-glycoproteins/N-glycopeptides differentially expressed between males and females. Metabolic pathway analysis was also carried out based on the kyoto encyclopedia of genes and genomes (KEGG). Differentially expressed N-glycoproteins were mostly associated with platelet degranulation, extracellular region, and ossification. The top three relevant pathways were glycan biosynthesis and metabolism, metabolism of cofactors and vitamins, and lipid metabolism. Overall, sex may be an important factor for urinary N-glycoproteome differences among normal individuals and should be considered in clinical applications. This study provides relevant information regarding the function and mechanisms of the urinary glycoproteome and the screening of clinical biomarkers.
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Affiliation(s)
- Shiting SHANG
- 军事科学院军事医学研究院生命组学研究所, 北京蛋白质组研究中心, 蛋白质组学国家重点实验室, 北京 102206
- Institute of Lifeomics, Academy of Military Medical Sciences, Academy of Military Sciences, Beijing Proteome Research Center, State Key Laboratory of Proteomics, Beijing 102206, China
| | - Hangyan DONG
- 军事科学院军事医学研究院生命组学研究所, 北京蛋白质组研究中心, 蛋白质组学国家重点实验室, 北京 102206
- Institute of Lifeomics, Academy of Military Medical Sciences, Academy of Military Sciences, Beijing Proteome Research Center, State Key Laboratory of Proteomics, Beijing 102206, China
| | - Yuanyuan LI
- 军事科学院军事医学研究院生命组学研究所, 北京蛋白质组研究中心, 蛋白质组学国家重点实验室, 北京 102206
- Institute of Lifeomics, Academy of Military Medical Sciences, Academy of Military Sciences, Beijing Proteome Research Center, State Key Laboratory of Proteomics, Beijing 102206, China
| | - Wanjun ZHANG
- 军事科学院军事医学研究院生命组学研究所, 北京蛋白质组研究中心, 蛋白质组学国家重点实验室, 北京 102206
- Institute of Lifeomics, Academy of Military Medical Sciences, Academy of Military Sciences, Beijing Proteome Research Center, State Key Laboratory of Proteomics, Beijing 102206, China
| | - Hang LI
- 军事科学院军事医学研究院生命组学研究所, 北京蛋白质组研究中心, 蛋白质组学国家重点实验室, 北京 102206
- Institute of Lifeomics, Academy of Military Medical Sciences, Academy of Military Sciences, Beijing Proteome Research Center, State Key Laboratory of Proteomics, Beijing 102206, China
| | - Weijie QIN
- 军事科学院军事医学研究院生命组学研究所, 北京蛋白质组研究中心, 蛋白质组学国家重点实验室, 北京 102206
- Institute of Lifeomics, Academy of Military Medical Sciences, Academy of Military Sciences, Beijing Proteome Research Center, State Key Laboratory of Proteomics, Beijing 102206, China
| | - Xiaohong QIAN
- 军事科学院军事医学研究院生命组学研究所, 北京蛋白质组研究中心, 蛋白质组学国家重点实验室, 北京 102206
- Institute of Lifeomics, Academy of Military Medical Sciences, Academy of Military Sciences, Beijing Proteome Research Center, State Key Laboratory of Proteomics, Beijing 102206, China
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21
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Wang S, Liu D, Qu J, Zhu H, Chen C, Gibbons C, Greenway H, Wang P, Bollag RJ, Liu K, Li L. Streamlined Subclass-Specific Absolute Quantification of Serum IgG Glycopeptides Using Synthetic Isotope-Labeled Standards. Anal Chem 2021; 93:4449-4455. [PMID: 33630567 PMCID: PMC8715724 DOI: 10.1021/acs.analchem.0c04462] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Absolute glycoproteomics quantification has drawn tremendous attention owing to its prospects in biomarker discovery and clinical implementation but is impeded by a general lack of suitable heavy isotope-labeled glycopeptide standards. In this study, we devised a facile chemoenzymatic strategy to synthesize a total of 36 human IgG glycopeptides attached with well-defined glycoforms, including 15 isotope-labeled ones with a mass increment of 6 Da to their native counterparts. Spiking of these standards into human sera enabled simplified, robust, and precise absolute quantification of IgG glycopeptides in a subclass-specific fashion. Additionally, the implementation of the absolute quantification approach revealed subclass-dependent alteration of serum IgG galactosylation and sialylation in colon cancer samples.
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Affiliation(s)
- Shuaishuai Wang
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Ding Liu
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Jingyao Qu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, Shandong, China
| | - He Zhu
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Congcong Chen
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Christopher Gibbons
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Harmon Greenway
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Peng Wang
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Roni J Bollag
- Department of Pathology, Augusta University, Augusta, Georgia 30912, United States
| | - Kebin Liu
- Department of Biochemistry and Molecular Biology, Augusta University, Augusta, Georgia 30912, United States
| | - Lei Li
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
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22
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Kalmar JG, Butler KE, Baker ES, Muddiman DC. Enhanced protocol for quantitative N-linked glycomics analysis using Individuality Normalization when Labeling with Isotopic Glycan Hydrazide Tags (INLIGHT)™. Anal Bioanal Chem 2020; 412:7569-7579. [PMID: 32844281 PMCID: PMC7541788 DOI: 10.1007/s00216-020-02892-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 08/09/2020] [Accepted: 08/17/2020] [Indexed: 01/10/2023]
Abstract
The analysis of N-linked glycans using liquid chromatography and mass spectrometry (LC-MS) presents significant challenges, particularly owing to their hydrophilic nature. To address these difficulties, a variety of derivatization methods have been developed to facilitate improved ionization and detection sensitivity. One such method, the Individuality Normalization when Labeling with Isotopic Glycan Hydrazide Tags (INLIGHT)™ strategy for labeling glycans, has previously been utilized in the analysis of N- and O-linked glycans in biological samples. To assess the maximum sensitivity and separability of the INLIGHT™ preparation and analysis pipeline, several critical steps were investigated. First, recombinant and nonrecombinant sources of PNGase F were compared to assess variations in the released glycans. Second, modifications in the INLIGHT™ derivatization step were evaluated including temperature optimization, solvent composition changes, reaction condition length and tag concentration. Optimization of the modified method resulted in 20-100 times greater peak areas for the detected N-linked glycans in fetuin and horseradish peroxidase compared with the standard method. Furthermore, the identification of low-abundance glycans, such as (Fuc)1(Gal)2(GlcNAc)4(Man)3(NeuAc)1 and (Gal)3(GlcNAc)5(Man)3(NeuAc)3, was possible. Finally, the optimal LC setup for the INLIGHT™ derivatized N-linked glycan analyses was found to be a C18 reverse-phase (RP) column with mobile phases typical of RPLC.
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Affiliation(s)
- Jaclyn Gowen Kalmar
- Department of Chemistry, North Carolina State University, Raleigh, NC, 27695, USA
| | - Karen E Butler
- Department of Chemistry, North Carolina State University, Raleigh, NC, 27695, USA
| | - Erin S Baker
- Department of Chemistry, North Carolina State University, Raleigh, NC, 27695, USA
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, 27695, USA
| | - David C Muddiman
- Department of Chemistry, North Carolina State University, Raleigh, NC, 27695, USA.
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, 27695, USA.
- Molecular Education, Technology, and Research Innovation Center (METRIC), North Carolina State University, Raleigh, NC, 27695, USA.
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23
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Bukke VN, Villani R, Archana M, Wawrzyniak A, Balawender K, Orkisz S, Ferraro L, Serviddio G, Cassano T. The Glucose Metabolic Pathway as A Potential Target for Therapeutics: Crucial Role of Glycosylation in Alzheimer's Disease. Int J Mol Sci 2020; 21:ijms21207739. [PMID: 33086751 PMCID: PMC7589651 DOI: 10.3390/ijms21207739] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 10/12/2020] [Accepted: 10/15/2020] [Indexed: 01/17/2023] Open
Abstract
Glucose uptake in the brain decreases because of normal aging but this decline is accelerated in Alzheimer’s disease (AD) patients. In fact, positron emission tomography (PET) studies have shown that metabolic reductions in AD patients occur decades before the onset of symptoms, suggesting that metabolic deficits may be an upstream event in at least some late-onset cases. A decrease in availability of glucose content induces a considerable impairment/downregulation of glycosylation, which is an important post-translational modification. Glycosylation is an important and highly regulated mechanism of secondary protein processing within cells and it plays a crucial role in modulating stability of proteins, as carbohydrates are important in achieving the proper three-dimensional conformation of glycoproteins. Moreover, glycosylation acts as a metabolic sensor that links glucose metabolism to normal neuronal functioning. All the proteins involved in β-amyloid (Aβ) precursor protein metabolism have been identified as candidates of glycosylation highlighting the possibility that Aβ metabolism could be regulated by their glycosylation. Within this framework, the present review aims to summarize the current understanding on the role of glycosylation in the etiopathology of AD, emphasizing the idea that glucose metabolic pathway may represent an alternative therapeutic option for targeting AD. From this perspective, the pharmacological modulation of glycosylation levels may represent a ‘sweet approach’ to treat AD targeting new mechanisms independent of the amyloid cascade and with comparable impacts in familial and sporadic AD.
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Affiliation(s)
- Vidyasagar Naik Bukke
- Department of Clinical and Experimental Medicine, University of Foggia, 71122 Foggia, Italy;
| | - Rosanna Villani
- Department of Medical and Surgical Sciences, University of Foggia, 71122 Foggia, Italy; (R.V.); (M.A.); (G.S.)
| | - Moola Archana
- Department of Medical and Surgical Sciences, University of Foggia, 71122 Foggia, Italy; (R.V.); (M.A.); (G.S.)
| | - Agata Wawrzyniak
- Morphological Science Department of Human Anatomy, Medical Faculty University of Rzeszów, 35-036 Rzeszów, Poland; (A.W.); (K.B.); (S.O.)
| | - Krzysztof Balawender
- Morphological Science Department of Human Anatomy, Medical Faculty University of Rzeszów, 35-036 Rzeszów, Poland; (A.W.); (K.B.); (S.O.)
| | - Stanislaw Orkisz
- Morphological Science Department of Human Anatomy, Medical Faculty University of Rzeszów, 35-036 Rzeszów, Poland; (A.W.); (K.B.); (S.O.)
| | - Luca Ferraro
- Department of Life Sciences and Biotechnology, University of Ferrara, 44100 Ferrara, Italy;
| | - Gaetano Serviddio
- Department of Medical and Surgical Sciences, University of Foggia, 71122 Foggia, Italy; (R.V.); (M.A.); (G.S.)
| | - Tommaso Cassano
- Department of Clinical and Experimental Medicine, University of Foggia, 71122 Foggia, Italy;
- Correspondence:
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24
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Wang H, Lu J, Gao WC, Ma X, Li N, Ding Z, Wu C, Zhu M, Qiao G, Xiao C, Zhang C, Chen C, Weng Z, Yang W, Zheng CB. Donepezil down-regulates propionylation, 2-hydroxyisobutyrylation, butyrylation, succinylation, and crotonylation in the brain of bilateral common carotid artery occlusion-induced vascular dementia rats. Clin Exp Pharmacol Physiol 2020; 47:1731-1739. [PMID: 32424975 DOI: 10.1111/1440-1681.13352] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 04/20/2020] [Accepted: 05/12/2020] [Indexed: 11/26/2022]
Abstract
Vascular dementia (VaD), caused by stroke or small vessel disease, is the second-most common type of dementia after Alzheimer's disease (AD). Donepezil is an acetylcholinesterase inhibitor that is currently used in patients with mild to moderate AD, and has recently been shown to improve cognitive performance in patients with VaD. In this study, we evaluated the effects of donepezil on VaD, and investigated the underlying molecular mechanisms of action. VaD was established by ligation of the bilateral common carotid artery occlusion (BCCAO). Executive function was tested by the Morris water maze (MWM) test and the attentional set shifting task (ASST). Our results showed that donepezil improved executive dysfunction and cognitive flexibility in BCCAO rats. In addition, we showed that donepezil treatment decreased the level of Aβ1-42 in BCCAO rats by enzyme-linked immunosorbent assay. Post-translational modifications (PTMs) are known to be critical mechanisms in the regulation of various cellular processes. Furthermore, PTMs have been linked to the central nervous system, which highlights the importance of PTMs in neurodegenerative diseases. In this study, we used western blot analysis to identify several novel PTMs in the hippocampus of BCCAO rats that were treated with or without donepezil. The data revealed that lysine propionylation, 2-hydroxyisobutyrylation, butyrylation, succinylation, and crotonylation were elevated in the hippocampus of BCCAO rats when compared to sham rats. This increase was abolished by donepezil treatment. Taken together, we speculate that donepezil treatment improves cognitive function in our animal model of VaD, possibly by reducing aberrant acyl-PTMs.
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Affiliation(s)
- Hongyan Wang
- School of Pharmaceutical Science and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming, China
| | - Jun Lu
- Department of Pharmacology, Guilin Medical University, Guilin, China
| | - Wen-Cong Gao
- School of Pharmaceutical Science and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming, China
| | - Xin Ma
- School of Pharmaceutical Science and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming, China
| | - Na Li
- School of Pharmaceutical Science and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming, China
| | - Zhituan Ding
- School of Pharmaceutical Science and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming, China
| | - Chunmei Wu
- School of Pharmaceutical Science and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming, China
| | - Maoceng Zhu
- School of Pharmaceutical Science and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming, China
| | - Guanrong Qiao
- School of Pharmaceutical Science and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming, China
| | - Chuang Xiao
- School of Pharmaceutical Science and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming, China
| | - Changhong Zhang
- School of Pharmaceutical Science and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming, China
| | - Chen Chen
- School of Pharmaceutical Science and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming, China
| | - Zhiying Weng
- School of Pharmaceutical Science and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming, China
| | - Weimin Yang
- School of Pharmaceutical Science and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming, China
| | - Chang-Bo Zheng
- School of Pharmaceutical Science and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming, China
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25
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Protein Expression Analysis of an In Vitro Murine Model of Prostate Cancer Progression: Towards Identification of High-Potential Therapeutic Targets. J Pers Med 2020; 10:jpm10030083. [PMID: 32784957 PMCID: PMC7565308 DOI: 10.3390/jpm10030083] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 07/15/2020] [Accepted: 07/27/2020] [Indexed: 12/11/2022] Open
Abstract
Background: Prostate cancer (PC) is the most frequently diagnosed cancer among men worldwide. The poor prognosis of PC is largely due to late diagnosis of the disease when it has progressed to advanced stages marked by androgen-independence. We interrogated proteomic signatures that embody the transition of PC from an androgen-dependent (AD) to an androgen-independent (AI) state. Methods: We have previously established AD and AI murine PC cell lines, PLum-AD and PLum-AI, respectively, which recapitulate primary and progressive PC at phenotypic and subcellular levels. We statistically surveyed global protein expression profiles in these cell lines. Differential profiles were functionally interrogated by pathways and protein–protein interaction network analyses. Results: Protein expression pattern analysis revealed a total of 683 proteins, among which 99 were significantly differentially altered in PLum-AI cells as compared to PLum-AD cells (45 increased and 54 decreased). Principal component analysis (PCA) revealed that the two different cell lines clearly separated apart, indicating a significant proteome expression difference between them. Four of the proteins (vimentin, catalase, EpCAM, and caspase 3) that were differentially expressed in PLum-AI cells compared to PLum-AD cells were subjected to biochemical validation by Western blotting. Biological process gene ontology (GO) analysis of the differentially expressed proteins demonstrated enrichment of biological functions and pathways in PLum-AI cells that are central to PI3 kinase and androgen receptor pathways. Besides, other relevant biological processes that are enriched in PLum-AI cells included cell adhesion and cell migration processes, cell and DNA damage, apoptosis, and cell cycle regulation. Conclusions: Our protein expression analysis of a murine in vitro model of PC progression identified differential protein spots that denote this progression and that comprise high-potential targets for early treatment of PC with a personalized patient-specific approach. Efforts are underway to functionally assess the potential roles of these proteins as therapeutic targets for PC progression.
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26
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Hronowski XL, Wang Y, Sosic Z, Wei R. On-MALDI-Target N-Glycan Nonreductive Amination by 2-Aminobenzoic Acid. Anal Chem 2020; 92:10252-10256. [PMID: 32628832 DOI: 10.1021/acs.analchem.0c01748] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
2-Aminobenzoic acid (2-AA) is widely used as a labeling reagent to derivatize released N-glycans at their free reducing terminus by reductive amination. 2-AA-labeled glycans have increased mass spectrometric sensitivity for their identification and enable fluorescence-chromatography-based glycan quantification. Drawbacks are that the labeling process is labor intensive and time consuming. Clean up of labeled glycans via removal of excess of labeling reagents often leads to sample losses. Here, we report use of 2-AA for labeling N-glycans on a MALDI target through nonreductive amination, while simultaneously functioning as a matrix in MALDI-MS glycan analysis. Coupling 2-AA to glycans results in significant increases of glycan anionic signals as compared to that using the traditional 2,5-dihydroxybenzoic acid (2,5-DHB) matrix. The on-MALDI-target sample preparation is a single-step protocol with high derivatization efficiency. It is also noticed that 2-AA-labeled glycan generated dominant deprotonated molecular anions with much fewer and low-intensity sodium adducts and therefore greatly simplified glycan profiles. We further explored its application in the N-glycan profile of a biotherapeutic monoclonal antibody and was able to achieve sensitive glycan identification at a low microgram level of glycoprotein. This 2-AA on-MALDI-target glycan derivatization eliminates tedious sample preparation and avoids sample loss. It is generally applicable for other applications (e.g., glycomics), where limited amounts of glycoproteins are available for analysis.
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27
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Zhu R, Huang Y, Zhao J, Zhong J, Mechref Y. Isomeric Separation of N-Glycopeptides Derived from Glycoproteins by Porous Graphitic Carbon (PGC) LC-MS/MS. Anal Chem 2020; 92:9556-9565. [PMID: 32544320 PMCID: PMC7815195 DOI: 10.1021/acs.analchem.0c00668] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Protein glycosylation is involved in many biological processes and physiological functions. Despite the recent advances in LC-MS/MS methodologies, the profiling of site-specific glycosylation is one of the major analytical challenges of glycoprotein analysis. Herein, we report that the separation of glycopeptide isomers on porous graphitic carbon (PGC)-LC was significantly improved by elevating the separation temperature under basic mobile phases. These findings permitted the isomeric separation of glycopeptides resulting from highly specific enzymatic digestions. The selectivity for different glycan types was studied using bovine fetuin, asialofetuin, IgG, ribonuclease B, and alpha-1 acid glycoprotein (AGP) by PGC-LC-MS. Comprehensive structural isomeric separation of glycopeptides was observed by high-resolution MS and confirmed by MS/MS. The specific structures of the glycopeptide isomers were identified and confirmed through exoglycosidase digestions. Glycosylation analysis of human AGP revealed the potential use of PGC-LC-MS for extensive glycoprotein analysis for biomarker discovery. This newly developed separation technique was shown as a reproducible and useful analytical method to study site-specific isomeric glycosylation.
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Affiliation(s)
| | | | - Jingfu Zhao
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX
| | - Jieqiang Zhong
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX
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28
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Dong X, Mondello S, Kobeissy F, Ferri R, Mechref Y. Serum Glycomics Profiling of Patients with Primary Restless Legs Syndrome Using LC–MS/MS. J Proteome Res 2020; 19:2933-2941. [DOI: 10.1021/acs.jproteome.9b00549] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Xue Dong
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United States
| | - Stefania Mondello
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Messina 98122, Italy
- Sleep Research Centre, Department of Neurology IC, Oasi Research Institute—IRCCS, Troina 94018, Italy
| | - Firas Kobeissy
- Department of Biochemistry & Molecular Genetics, American University of Beirut, Beirut 1107 2020, Lebanon
| | - Raffaele Ferri
- Sleep Research Centre, Department of Neurology IC, Oasi Research Institute—IRCCS, Troina 94018, Italy
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United States
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29
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Protein Degradome of Spinal Cord Injury: Biomarkers and Potential Therapeutic Targets. Mol Neurobiol 2020; 57:2702-2726. [PMID: 32328876 DOI: 10.1007/s12035-020-01916-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 03/31/2020] [Indexed: 12/13/2022]
Abstract
Degradomics is a proteomics sub-discipline whose goal is to identify and characterize protease-substrate repertoires. With the aim of deciphering and characterizing key signature breakdown products, degradomics emerged to define encryptic biomarker neoproteins specific to certain disease processes. Remarkable improvements in structural and analytical experimental methodologies as evident in research investigating cellular behavior in neuroscience and cancer have allowed the identification of specific degradomes, increasing our knowledge about proteases and their regulators and substrates along with their implications in health and disease. A physiologic balance between protein synthesis and degradation is sought with the activation of proteolytic enzymes such as calpains, caspases, cathepsins, and matrix metalloproteinases. Proteolysis is essential for development, growth, and regeneration; however, inappropriate and uncontrolled activation of the proteolytic system renders the diseased tissue susceptible to further neurotoxic processes. In this article, we aim to review the protease-substrate repertoires as well as emerging therapeutic interventions in spinal cord injury at the degradomic level. Several protease substrates and their breakdown products, essential for the neuronal structural integrity and functional capacity, have been characterized in neurotrauma including cytoskeletal proteins, neuronal extracellular matrix glycoproteins, cell junction proteins, and ion channels. Therefore, targeting exaggerated protease activity provides a potentially effective therapeutic approach in the management of protease-mediated neurotoxicity in reducing the extent of damage secondary to spinal cord injury.
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30
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Wang W, Gopal S, Pocock R, Xiao Z. Glycan Mimetics from Natural Products: New Therapeutic Opportunities for Neurodegenerative Disease. Molecules 2019; 24:molecules24244604. [PMID: 31888221 PMCID: PMC6943557 DOI: 10.3390/molecules24244604] [Citation(s) in RCA: 18] [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: 09/26/2019] [Revised: 12/12/2019] [Accepted: 12/13/2019] [Indexed: 12/20/2022] Open
Abstract
Neurodegenerative diseases (NDs) affect millions of people worldwide. Characterized by the functional loss and death of neurons, NDs lead to symptoms (dementia and seizures) that affect the daily lives of patients. In spite of extensive research into NDs, the number of approved drugs for their treatment remains limited. There is therefore an urgent need to develop new approaches for the prevention and treatment of NDs. Glycans (carbohydrate chains) are ubiquitous, abundant, and structural complex natural biopolymers. Glycans often covalently attach to proteins and lipids to regulate cellular recognition, adhesion, and signaling. The importance of glycans in both the developing and mature nervous system is well characterized. Moreover, glycan dysregulation has been observed in NDs such as Alzheimer's disease (AD), Huntington's disease (HD), Parkinson's disease (PD), multiple sclerosis (MS), and amyotrophic lateral sclerosis (ALS). Therefore, glycans are promising but underexploited therapeutic targets. In this review, we summarize the current understanding of glycans in NDs. We also discuss a number of natural products that functionally mimic glycans to protect neurons, which therefore represent promising new therapeutic approaches for patients with NDs.
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31
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Wu H, Kohler J. Photocrosslinking probes for capture of carbohydrate interactions. Curr Opin Chem Biol 2019; 53:173-182. [PMID: 31706134 DOI: 10.1016/j.cbpa.2019.09.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 09/13/2019] [Accepted: 09/17/2019] [Indexed: 01/03/2023]
Abstract
Glycan-mediated interactions are essential in many biological processes and regulate a wide variety of cellular functions. However, characterizing these interactions is difficult because glycan biosynthesis is not template driven and because carbohydrate recognition events are usually of low affinity and transient. Photocrosslinking carbohydrate probes can form a covalent bond with molecules in close proximity on UV irradiation and are capable of capturing interactions between glycans and glycan-binding proteins in situ. Because of these advantages, multiple photocrosslinking carbohydrate probes have been designed and applied to study the biological functions of glycans. This review will discuss recent advances in the development of novel photocrosslinking functional groups and the design of photocrosslinking probes to detect interactions mediated by glycolipids, peptidoglycan, and multivalent carbohydrate ligands. These probes have demonstrated the potential to address some of the major challenges in the study of glycan-mediated interactions in both model systems and in more complex biological settings.
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Affiliation(s)
- Han Wu
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jennifer Kohler
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, TX 75390, USA. http://
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32
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Dong X, Peng W, Yu CY, Zhou S, Donohoo KB, Tang H, Mechref Y. 8-plex LC-MS/MS Analysis of Permethylated N-Glycans Achieved by Using Stable Isotopic Iodomethane. Anal Chem 2019; 91:11794-11802. [PMID: 31356052 PMCID: PMC7412976 DOI: 10.1021/acs.analchem.9b02411] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Glycosylation is an important post-translational modification of proteins. Many diseases, such as cancer, have proved to be related to aberrant glycosylation. High throughput quantitative methods have gained attention recently in the study of glycomics. With the development of high-resolution mass spectrometry, the sensitivity of detection in glycomics has largely improved; however, most of the commonly used MS-based techniques are focused on relative quantitative analysis, which can hardly provide direct comparative glycomic quantitation results. In this study, we developed a novel multiplex glycomic analysis method on an LC-ESI-MS platform. Reduced glycans were stable isotopic labeled during the permethylation procedure, with the use of iodomethane reagents CH2DI, CHD2I, CD3I, 13CH3I, 13CH2DI, 13CHD2I, 13CD3I, and CH3I. Up to 8-plex glycomic profiling was possible in a single analysis by LC-MS, and a 100 k mass resolution was sufficient to allow a baseline resolution of the mass differences among the 8-plex labeled glycans. The major advantages of this method are that it overcomes quantitative fluctuations caused by nanoESI, it facilitates a level of comparative quantitative glycomic analysis that accurately reflects the quantitative information in samples, and it dramatically shortens analysis time. Quantitation validation was tested on glycans released from bovine fetuin and model glycoprotein mixtures (RNase B, bovine fetuin, and IgG) with good linearity (R2 = 0.9884) and a dynamic range from 0.1 to 10. The 8-plex strategy was successfully applied to a comparative glycomic study of cancer cell lines. The results demonstrate that different distributions of sialylated glycans are related to the metastatic properties of cell lines and provide important clues for a better understanding of breast cancer brain metastasis.
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Affiliation(s)
- Xue Dong
- Department of Chemistry & Biochemistry, Texas Tech University, Lubbock, Texas, 79409, United States
| | - Wenjing Peng
- Department of Chemistry & Biochemistry, Texas Tech University, Lubbock, Texas, 79409, United States
| | - Chuan-Yih Yu
- School of Informatics & Computing, Indiana University, Bloomington, Indiana, 47408, United States
| | - Shiyue Zhou
- Department of Chemistry & Biochemistry, Texas Tech University, Lubbock, Texas, 79409, United States
| | - Kaitlyn B. Donohoo
- Department of Chemistry & Biochemistry, Texas Tech University, Lubbock, Texas, 79409, United States
| | - Haixu Tang
- School of Informatics & Computing, Indiana University, Bloomington, Indiana, 47408, United States
| | - Yehia Mechref
- Department of Chemistry & Biochemistry, Texas Tech University, Lubbock, Texas, 79409, United States
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33
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Lane CS, McManus K, Widdowson P, Flowers SA, Powell G, Anderson I, Campbell JL. Separation of Sialylated Glycan Isomers by Differential Mobility Spectrometry. Anal Chem 2019; 91:9916-9924. [PMID: 31283185 PMCID: PMC6686149 DOI: 10.1021/acs.analchem.9b01595] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Accepted: 06/18/2019] [Indexed: 12/28/2022]
Abstract
Mass spectrometry has proven itself to be an important technology for characterizing intact glycoproteins, glycopeptides, and released glycans. However, these molecules often present significant challenges during analysis. For example, glycans of identical molecular weights can be present in many isomeric forms, with one form having dramatically more biological activity than the others. Discriminating among these isomeric forms using mass spectrometry alone can be daunting, which is why orthogonal techniques, such as ion mobility spectrometry, have been explored. Here, we demonstrate the use of differential mobility spectrometry (DMS) to separate isomeric glycans differing only in the linkages of sialic acid groups (e.g., α 2,3 versus α 2,6). This ability extends from a small trisaccharide species to larger biantennary systems and is driven, in part, by the role of intramolecular solvation of the charge site(s) on these ions within the DMS environment.
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Affiliation(s)
- Catherine S. Lane
- SCIEX, Phoenix House, Centre Park, Warrington WA1 1RX, United Kingdom
| | - Kirsty McManus
- Allergan
Biologics Limited, 12 Estuary Banks, Speke, Liverpool L24 8RB, United Kingdom
| | - Philip Widdowson
- Allergan
Biologics Limited, 12 Estuary Banks, Speke, Liverpool L24 8RB, United Kingdom
| | | | - Gerard Powell
- Allergan
Biologics Limited, 12 Estuary Banks, Speke, Liverpool L24 8RB, United Kingdom
| | - Ian Anderson
- Allergan
Biologics Limited, 12 Estuary Banks, Speke, Liverpool L24 8RB, United Kingdom
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Szczubiał M, Wawrzykowski J, Dąbrowski R, Bochniarz M, Brodzki P, Kankofer M. The effect of pyometra on glycosylation of proteins in the uterine tissues from female dogs. Theriogenology 2019; 131:41-46. [PMID: 30939355 DOI: 10.1016/j.theriogenology.2019.03.020] [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] [Received: 01/10/2019] [Revised: 03/20/2019] [Accepted: 03/24/2019] [Indexed: 12/26/2022]
Abstract
The main aim of this study was to investigate the effect of pyometra on glycosylation of proteins in the uterine tissues from female dogs, using western blotting with selected lectins (Sambucus nigra agglutinin - SNA and Maackia amurensis agglutinin - MAL II). In addition protein pattern of examined tissues was also evaluated. The study was performed on 10 female dogs undergoing ovariohysterectomy because of pyometra and 10 clinically healthy female dogs, undergoing elective spaying (ovariohysterectomy). Uterine tissue samples of 1 cm2 were taken from the middle region of each uterine horn in both group of animals immediately after ovariohysterectomy. Tissue samples were homogenized and analysed by sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) and western blotting with SNA and MAL II. SDS-PAGE analysis showed differences between pyometra samples and controls in the amount of obtained protein fractions and the protein content in the individual fractions. Five protein (with a molecular weight of 193.78 kDa, 103.18 kDa, 77.67 kDa, 70.39 kDa, and 53.00 kDa) were found only in the pyometra samples. The remaining fractions differed in intensity of staining, which indicated differ abundance of a given protein. The results of western blotting with SNA and MAL II demonstrated that the pattern obtained from densitometric analysis differs between adequate healthy and pyometra samples with regard to the amount of protein fraction obtained as well as the intensity of staining of particular fraction. The pyometra tissues contained seven SNA-binding proteins (with a molecular weight 189.94 kDa, 165.51 kDa, 100.94 kDa, 59.42 KDa, 41.32 kDa, 35.16 kDa, and 32.6 kDa) that were not in the healthy tissues. Of the nine remaining fractions, six showed significantly higher (P < 0.05) intensity of staining in the healthy uterine tissues. In turn, the MAL II-binding protein with a molecular weight 75.85 kDa, 51.12 kDa, and 49.98 kDa were found only in the pyometra samples. Of the 28 remaining fractions, ten demonstrated significantly higher (P < 0.05), and five fractions had significantly lower (P < 0.05) intensity of staining in the pyometra tissues. The results obtained indicate that proteins in uterine tissues from female dogs with pyometra are differently glycosylated compared to normal uterine tissues. These findings provide the basis for further studies of the possible role of glycosylation in the pathogenesis of canine pyometra.
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Affiliation(s)
- Marek Szczubiał
- Department and Clinic of Animal Reproduction, Faculty of Veterinary Medicine, University of Life Sciences, Głeboka 30, 20-612, Lublin, Poland.
| | - Jacek Wawrzykowski
- Department of Animal Biochemistry, Faculty of Veterinary Medicine, University of Life Sciences, Akademicka 12, 20-033, Lublin, Poland
| | - Roman Dąbrowski
- Department and Clinic of Animal Reproduction, Faculty of Veterinary Medicine, University of Life Sciences, Głeboka 30, 20-612, Lublin, Poland
| | - Mariola Bochniarz
- Department and Clinic of Animal Reproduction, Faculty of Veterinary Medicine, University of Life Sciences, Głeboka 30, 20-612, Lublin, Poland
| | - Piotr Brodzki
- Department and Clinic of Animal Reproduction, Faculty of Veterinary Medicine, University of Life Sciences, Głeboka 30, 20-612, Lublin, Poland
| | - Marta Kankofer
- Department of Animal Biochemistry, Faculty of Veterinary Medicine, University of Life Sciences, Akademicka 12, 20-033, Lublin, Poland
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Kaur S, Baldi B, Vuong J, O'Donoghue SI. Visualization and Analysis of Epiproteome Dynamics. J Mol Biol 2019; 431:1519-1539. [PMID: 30769119 DOI: 10.1016/j.jmb.2019.01.044] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 01/29/2019] [Accepted: 01/29/2019] [Indexed: 12/28/2022]
Abstract
The epiproteome describes the set of all post-translational modifications (PTMs) made to the proteins comprising a cell or organism. The extent of the epiproteome is still largely unknown; however, advances in experimental techniques are beginning to produce a deluge of data, tracking dynamic changes to the epiproteome in response to cellular stimuli. These data have potential to revolutionize our understanding of biology and disease. This review covers a range of recent visualization methods and tools developed specifically for dynamic epiproteome data sets. These methods have been designed primarily for data sets on phosphorylation, as this the most studied PTM; however, most of these methods are also applicable to other types of PTMs. Unfortunately, the currently available methods are often inadequate for existing data sets; thus, realizing the potential buried in epiproteome data sets will require new, tailored bioinformatics methods that will help researchers analyze, visualize, and interactively explore these complex data sets.
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Affiliation(s)
- Sandeep Kaur
- University of New South Wales (UNSW), Kensington, NSW 2052, Australia; Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia.
| | - Benedetta Baldi
- Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia; Data 61, CSIRO, Eveleigh, NSW 2015, Australia.
| | - Jenny Vuong
- Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia; Data 61, CSIRO, Eveleigh, NSW 2015, Australia.
| | - Seán I O'Donoghue
- University of New South Wales (UNSW), Kensington, NSW 2052, Australia; Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia; Data 61, CSIRO, Eveleigh, NSW 2015, Australia.
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Pascovici D, Wu JX, McKay MJ, Joseph C, Noor Z, Kamath K, Wu Y, Ranganathan S, Gupta V, Mirzaei M. Clinically Relevant Post-Translational Modification Analyses-Maturing Workflows and Bioinformatics Tools. Int J Mol Sci 2018; 20:E16. [PMID: 30577541 PMCID: PMC6337699 DOI: 10.3390/ijms20010016] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 12/09/2018] [Accepted: 12/17/2018] [Indexed: 01/04/2023] Open
Abstract
Post-translational modifications (PTMs) can occur soon after translation or at any stage in the lifecycle of a given protein, and they may help regulate protein folding, stability, cellular localisation, activity, or the interactions proteins have with other proteins or biomolecular species. PTMs are crucial to our functional understanding of biology, and new quantitative mass spectrometry (MS) and bioinformatics workflows are maturing both in labelled multiplexed and label-free techniques, offering increasing coverage and new opportunities to study human health and disease. Techniques such as Data Independent Acquisition (DIA) are emerging as promising approaches due to their re-mining capability. Many bioinformatics tools have been developed to support the analysis of PTMs by mass spectrometry, from prediction and identifying PTM site assignment, open searches enabling better mining of unassigned mass spectra-many of which likely harbour PTMs-through to understanding PTM associations and interactions. The remaining challenge lies in extracting functional information from clinically relevant PTM studies. This review focuses on canvassing the options and progress of PTM analysis for large quantitative studies, from choosing the platform, through to data analysis, with an emphasis on clinically relevant samples such as plasma and other body fluids, and well-established tools and options for data interpretation.
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Affiliation(s)
- Dana Pascovici
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
- Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW 2109, Australia.
| | - Jemma X Wu
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
- Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW 2109, Australia.
| | - Matthew J McKay
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
- Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW 2109, Australia.
| | - Chitra Joseph
- Department of Clinical Medicine, Macquarie University, Sydney, NSW 2109, Australia.
| | - Zainab Noor
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
| | - Karthik Kamath
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
- Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW 2109, Australia.
| | - Yunqi Wu
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
- Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW 2109, Australia.
| | - Shoba Ranganathan
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
| | - Vivek Gupta
- Department of Clinical Medicine, Macquarie University, Sydney, NSW 2109, Australia.
| | - Mehdi Mirzaei
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
- Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW 2109, Australia.
- Department of Clinical Medicine, Macquarie University, Sydney, NSW 2109, Australia.
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Dong X, Mondello S, Kobeissy F, Talih F, Ferri R, Mechref Y. LC-MS/MS glycomics of idiopathic rapid eye movement sleep behavior disorder. Electrophoresis 2018; 39:3096-3103. [PMID: 30168606 PMCID: PMC6625764 DOI: 10.1002/elps.201800316] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 08/20/2018] [Accepted: 08/20/2018] [Indexed: 12/15/2022]
Abstract
Idiopathic REM sleep behavior disorder (iRBD) is now considered a prodromal stage of an α-synucleinopathy-related to neurodegenerative disease such as Parkinson's diseases. Emerging evidence has shown that post-translational modification or glycosylation are implicated in dynamic disease mechanisms and the onset of many pathological conditions. We hypothesized that the characterization of the glycosylation pattern of patients with RBD would be of great value to understand the pathophysiology and underlying mechanisms and represent potentially useful biomarkers for disease-associated molecular changes. To test this hypothesis, we assessed the serum glycome of patients with RBD and compared to that of healthy controls. NanoRPLC-MS was used to generate quantitative N-glycan profiles while high-temperature PGC-LC-MS platform was employed to generate quantitative isomeric N-glycan profiles. By analyzing permethylated glycans derived from human blood sera on C18-LC-MS/MS, we identified 59 N-glycan structures in healthy (control) cohort, 56 N-glycans in RBD cohort. Sixteen N-glycans structures were found to be significantly altered in the RBD cohort (p < 0.05). N-glycans with the composition of HexNAc4 Hex5 Fuc1 , HexNAc5 Hex5 , and HexNAc4 Hex5 Fuc1 NeuAc1 presented the most substantial difference between controls and RBD patients (p < 0.01). HexNAc4 Hex5 Fuc1 NeuAc1 showed a relatively high abundance (3.1 ± 0.7% in the control cohort versus 4 ± 3% in the idiopathic RBD cohort). These N-glycans can be potential diagnostic biomarker candidates and provide a window into underlying neurodegenerative processes in patients with idiopathic RBD. In addition, 7 N-glycan isomers were significantly different between controls and RBD patients (p < 0.05). HexNAc4 Hex5 Fuc1 NeuAc1 (4511-2) and HexNAc4 Hex5 Fuc1 NeuAc2 (4512-2) showed the most substantial difference between the control and idiopathic RBD cohorts (p < 0.001). Levels of both these two isomeric structures were higher in the idiopathic RBD cohort. Further larger studies are required to assess the reproducibility of these findings and to elucidate the role played by the changes in glycan structures in the pathogenetic mechanisms of RBD. This information will be instrumental in developing molecular therapeutic targets to promote neuroprotection and prevention of neurodegeneration.
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Affiliation(s)
- Xue Dong
- Department of Chemistry and Biochemistry, Texas Tech University
| | - Stefania Mondello
- Sleep Research Centre, Department of Neurology IC, Oasi Research Institute- IRCCS, Troina, Italy
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Messina, Italy
| | - Firas Kobeissy
- Department of Biochemistry & Molecular Genetics, American University of Beirut, Beirut, Lebanon
| | - Farid Talih
- Department of Psychiatry, American University of Beirut, Beirut, Lebanon
| | - Raffaele Ferri
- Sleep Research Centre, Department of Neurology IC, Oasi Research Institute- IRCCS, Troina, Italy
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University
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Niwa Y, Simizu S. C-Mannosylation: Previous Studies and Future Research Perspectives. TRENDS GLYCOSCI GLYC 2018. [DOI: 10.4052/tigg.1755.1j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Yuki Niwa
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University
| | - Siro Simizu
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University
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Niwa Y, Simizu S. C-Mannosylation: Previous Studies and Future Research Perspectives. TRENDS GLYCOSCI GLYC 2018. [DOI: 10.4052/tigg.1755.1e] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Yuki Niwa
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University
| | - Siro Simizu
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University
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Zhang Q, Li Z, Wang Y, Zheng Q, Li J. Mass spectrometry for protein sialoglycosylation. MASS SPECTROMETRY REVIEWS 2018; 37:652-680. [PMID: 29228471 DOI: 10.1002/mas.21555] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 11/17/2017] [Indexed: 06/07/2023]
Abstract
Sialic acids are a family of structurally unique and negatively charged nine-carbon sugars, normally found at the terminal positions of glycan chains on glycoproteins and glycolipids. The glycosylation of proteins is a universal post-translational modification in eukaryotic species and regulates essential biological functions, in which the most common sialic acid is N-acetyl-neuraminic acid (2-keto-5-acetamido-3,5-dideoxy-D-glycero-D-galactononulopyranos-1-onic acid) (Neu5NAc). Because of the properties of sialic acids under general mass spectrometry (MS) conditions, such as instability, ionization discrimination, and mixed adducts, the use of MS in the analysis of protein sialoglycosylation is still challenging. The present review is focused on the application of MS related methodologies to the study of both N- and O-linked sialoglycans. We reviewed MS-based strategies for characterizing sialylation by analyzing intact glycoproteins, proteolytic digested glycopeptides, and released glycans. The review concludes with future perspectives in the field.
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Affiliation(s)
- Qiwei Zhang
- Key Laboratory of Optoelectronic Chemical Materials and Devices of Ministry of Education, Institute for Interdisciplinary Research, Institute of Environment and Health, School of Chemical and Environmental Engineering, Jianghan University, Wuhan, China
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Haidian District, Beijing, China
| | - Zack Li
- School of Medicine, Queen's University, Kingston, Ontario, Canada
| | - Yawei Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Haidian District, Beijing, China
| | - Qi Zheng
- Key Laboratory of Optoelectronic Chemical Materials and Devices of Ministry of Education, Institute for Interdisciplinary Research, Institute of Environment and Health, School of Chemical and Environmental Engineering, Jianghan University, Wuhan, China
| | - Jianjun Li
- National Research Council Canada, Ottawa, Ontario, Canada
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41
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Banazadeh A, Peng W, Veillon L, Mechref Y. Carbon Nanoparticles and Graphene Nanosheets as MALDI Matrices in Glycomics: a New Approach to Improve Glycan Profiling in Biological Samples. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:1892-1900. [PMID: 29916086 PMCID: PMC6298861 DOI: 10.1007/s13361-018-1985-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 04/28/2018] [Accepted: 04/28/2018] [Indexed: 05/15/2023]
Abstract
Glycomics continues to be a highly dynamic and interesting research area due to the need to comprehensively understand the biological attributes of glycosylation in many important biological functions such as the immune response, cell development, cell differentiation/adhesion, and host-pathogen interactions. Although matrix-assisted laser desorption ionization (MALDI) mass spectrometry (MS) has proven to be suitable for glycomic profiling studies, there is a need for improved sensitivity in the detection of native glycans, which ionize inefficiently. In this study, we investigated the efficiencies of graphene nanosheets (GNs) and carbon nanoparticles (CNPs) as MALDI matrices and co-matrices in glycan profiling. Our results indicated an enhancement of signal intensity by several orders of magnitude upon using GNs and CNPs in MALDI analysis of N-glycans derived from a variety of biological samples. Interestingly, increasing the amounts of CNPs and GNs improved not only the signal intensities but also prompted in-source decay (ISD) fragmentations, which produced extensive glycosidic and cross-ring cleavages. Our results indicated that the extent of ISD fragmentation could be modulated by CNP and GN concentrations, to obtain MS2 and pseudo-MS3 spectra. The results for glycan profiling in high salt solutions confirmed high salt-tolerance capacities for both CNPs and GNs. Finally, the results showed that by using CNPs and GNs as co-matrices, DHB crystal formation was more homogeneous which improved shot-to-shot reproducibility and sensitivity. Graphical Abstract ᅟ.
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Affiliation(s)
- Alireza Banazadeh
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, 79409-1061, USA
| | - Wenjing Peng
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, 79409-1061, USA
| | - Lucas Veillon
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, 79409-1061, USA
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, 79409-1061, USA.
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Sharma S, Young RJ, Chen J, Chen X, Oh EC, Schiller MR. Minimotifs dysfunction is pervasive in neurodegenerative disorders. ALZHEIMER'S & DEMENTIA (NEW YORK, N. Y.) 2018; 4:414-432. [PMID: 30225339 PMCID: PMC6139474 DOI: 10.1016/j.trci.2018.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Minimotifs are modular contiguous peptide sequences in proteins that are important for posttranslational modifications, binding to other molecules, and trafficking to specific subcellular compartments. Some molecular functions of proteins in cellular pathways can be predicted from minimotif consensus sequences identified through experimentation. While a role for minimotifs in regulating signal transduction and gene regulation during disease pathogenesis (such as infectious diseases and cancer) is established, the therapeutic use of minimotif mimetic drugs is limited. In this review, we discuss a general theme identifying a pervasive role of minimotifs in the pathomechanism of neurodegenerative diseases. Beyond their longstanding history in the genetics of familial neurodegeneration, minimotifs are also major players in neurotoxic protein aggregation, aberrant protein trafficking, and epigenetic regulation. Generalizing the importance of minimotifs in neurodegenerative diseases offers a new perspective for the future study of neurodegenerative mechanisms and the investigation of new therapeutics.
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Affiliation(s)
- Surbhi Sharma
- Nevada Institute of Personalized Medicine, Las Vegas, NV, USA
- School of Life Sciences, Las Vegas, NV, USA
| | - Richard J. Young
- Nevada Institute of Personalized Medicine, Las Vegas, NV, USA
- School of Life Sciences, Las Vegas, NV, USA
| | - Jingchun Chen
- Nevada Institute of Personalized Medicine, Las Vegas, NV, USA
| | - Xiangning Chen
- Nevada Institute of Personalized Medicine, Las Vegas, NV, USA
- Department of Psychology, Las Vegas, NV, USA
| | - Edwin C. Oh
- Nevada Institute of Personalized Medicine, Las Vegas, NV, USA
- School of Medicine, Las Vegas, NV, USA
| | - Martin R. Schiller
- Nevada Institute of Personalized Medicine, Las Vegas, NV, USA
- School of Life Sciences, Las Vegas, NV, USA
- School of Medicine, Las Vegas, NV, USA
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Zhu R, Zhou S, Peng W, Huang Y, Mirzaei P, Donohoo K, Mechref Y. Enhanced Quantitative LC-MS/MS Analysis of N-linked Glycans Derived from Glycoproteins Using Sodium Deoxycholate Detergent. J Proteome Res 2018; 17:2668-2678. [PMID: 29745666 DOI: 10.1021/acs.jproteome.8b00127] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Protein glycosylation is a common protein post-translational modification (PTM) in living organisms and has been shown to associate with multiple diseases, and thus may potentially be a biomarker of such diseases. Efficient protein/glycoprotein extraction is a crucial step in the preparation of N-glycans derived from glycoproteins prior to LC-MS analysis. Convenient, efficient and unbiased sample preparation protocols are needed. Herein, we evaluated the use of sodium deoxycholate (SDC) acidic labile detergent to release N-glycans of glycoproteins derived from biological samples such as cancer cell lines. Compared to the filter-aided sample preparation approach, the sodium deoxycholate (SDC) assisted approach was determined to be more efficient and unbiased. SDC removal was determined to be more efficient when using acidic precipitation rather than ethyl acetate phase transfer. Efficient extraction of proteins/glycoproteins from biological samples was achieved by combining SDC lysis buffer and beads beating cell disruption. This was suggested by a significant overall increase in the intensities of N-glycans released from cancer cell lines. Additionally, the use of SDC approach was also shown to be more reproducible than those methods that do not use SDC.
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Affiliation(s)
- Rui Zhu
- Department of Chemistry and Biochemistry , Texas Tech University , Lubbock , Texas 79409 , United States
| | - Shiyue Zhou
- Department of Chemistry and Biochemistry , Texas Tech University , Lubbock , Texas 79409 , United States
| | - Wenjing Peng
- Department of Chemistry and Biochemistry , Texas Tech University , Lubbock , Texas 79409 , United States
| | - Yifan Huang
- Department of Chemistry and Biochemistry , Texas Tech University , Lubbock , Texas 79409 , United States
| | - Parvin Mirzaei
- Department of Chemistry and Biochemistry , Texas Tech University , Lubbock , Texas 79409 , United States
| | - Kaitlyn Donohoo
- Department of Chemistry and Biochemistry , Texas Tech University , Lubbock , Texas 79409 , United States
| | - Yehia Mechref
- Department of Chemistry and Biochemistry , Texas Tech University , Lubbock , Texas 79409 , United States
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Qu Y, Sun L, Zhang Z, Dovichi NJ. Site-Specific Glycan Heterogeneity Characterization by Hydrophilic Interaction Liquid Chromatography Solid-Phase Extraction, Reversed-Phase Liquid Chromatography Fractionation, and Capillary Zone Electrophoresis-Electrospray Ionization-Tandem Mass Spectrometry. Anal Chem 2018; 90:1223-1233. [PMID: 29231704 PMCID: PMC5771954 DOI: 10.1021/acs.analchem.7b03912] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Reversed-phase chromatographic separation of glycopeptides tends to be dominated by the peptide composition. In contrast, capillary zone electrophoresis separation of glycopeptides is particularly sensitive to the sialic acid composition of the glycan. In this paper, we combine the two techniques to achieve superior N-glycopeptide analysis. Glycopeptides were first isolated from a tryptic digest using hydrophilic interaction liquid chromatography (HILIC) solid-phase extraction. The glycopeptides were separated using reversed-phase ultra high-performance liquid chromatography (UHPLC) to generate four fractions corresponding to different peptide backbones. Capillary zone electrophoresis-electrospray ionization-tandem mass spectrometry (CZE-ESI-MS/MS) was used to analyze the fractions. We applied this method for the analysis of alpha-1-acid glycoprotein (AGP). A total of 268 site-specific N-glycopeptides were detected, representing eight different glycosylation sites from two isomers of AGP. Glycans included tetra-sialic acids with multi N-acetyllactosamine (LacNAc) repeats and unusual pentasialylated terminal sialic acids. Reversed-phase UHPLC coupled with CZE generated ∼35% more N-glycopeptides than direct reversed-phase UHPLC-ESI-MS/MS analysis and ∼70% more N-glycopeptides than direct CZE-ESI-MS/MS analysis. This approach is a promising tool for global, site-specific glycosylation analysis of highly heterogeneous glycoproteins with mass-limited samples.
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Affiliation(s)
- Yanyan Qu
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Liangliang Sun
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - Zhenbin Zhang
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Norman J. Dovichi
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
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Barroso A, Giménez E, Konijnenberg A, Sancho J, Sanz-Nebot V, Sobott F. Evaluation of ion mobility for the separation of glycoconjugate isomers due to different types of sialic acid linkage, at the intact glycoprotein, glycopeptide and glycan level. J Proteomics 2017; 173:22-31. [PMID: 29197583 DOI: 10.1016/j.jprot.2017.11.020] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 11/23/2017] [Accepted: 11/24/2017] [Indexed: 02/07/2023]
Abstract
The study of protein glycosylation can be regarded as an intricate but very important task, making glycomics one of the most challenging and interesting, albeit under-researched, type of "omics" science. Complexity escalates remarkably when considering that carbohydrates can form severely branched structures with many different constituents, which often leads to the formation of multiple isomers. In this regard, ion mobility (IM) spectrometry has recently demonstrated its power for the separation of isomeric compounds. In the present work, the potential of traveling wave IM (TWIMS) for the separation of isomeric glycoconjugates was evaluated, using mouse transferrin (mTf) as model glycoprotein. Particularly, we aim to assess the performance of this platform for the separation of isomeric glycoconjugates due to the type of sialic acid linkage, at the intact glycoprotein, glycopeptide and glycan level. Straightforward separation of isomers was achieved with the analysis of released glycans, as opposed to the glycopeptides which showed a more complex pattern. Finally, the developed methodology was applied to serum samples of mice, to investigate its robustness when analyzing real complex samples. BIOLOGICAL SIGNIFICANCE Ion mobility mass spectrometry is a promising analytical technique for the separation of glycoconjugate isomers due to type of sialic acid linkage. The impact of such a small modification in the glycan structure is more evident in smaller analytes, reason why the analysis of free glycans was easier compared to the intact protein or the glycopeptides. The established methodology could be regarded as starting point in the separation of highly decorated glycoconjugates. This is an important topic nowadays, as differences in the abundance of some glycan isomers could be the key for the early diagnosis, control or differentiation of certain diseases, such as inflammation or cancer.
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Affiliation(s)
- Albert Barroso
- Department of Chemical Engineering and Analytical Chemistry, University of Barcelona, Diagonal 645, 08028 Barcelona, Spain
| | - Estela Giménez
- Department of Chemical Engineering and Analytical Chemistry, University of Barcelona, Diagonal 645, 08028 Barcelona, Spain.
| | - Albert Konijnenberg
- Biomolecular & Analytical Mass Spectrometry Group, Department of Chemistry, University of Antwerp, Antwerp, Belgium
| | - Jaime Sancho
- Instituto de Parasitología y Biomedicina "López-Neyra" (IPBLN), CSIC, Armilla, Granada, Spain
| | - Victoria Sanz-Nebot
- Department of Chemical Engineering and Analytical Chemistry, University of Barcelona, Diagonal 645, 08028 Barcelona, Spain
| | - Frank Sobott
- Biomolecular & Analytical Mass Spectrometry Group, Department of Chemistry, University of Antwerp, Antwerp, Belgium; Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom; School of Molecular and Cellular Biology, University of Leeds, LS2 9JT, United Kingdom.
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Gutierrez Najera NA, Resendis-Antonio O, Nicolini H. "Gestaltomics": Systems Biology Schemes for the Study of Neuropsychiatric Diseases. Front Physiol 2017; 8:286. [PMID: 28536537 PMCID: PMC5422874 DOI: 10.3389/fphys.2017.00286] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 04/19/2017] [Indexed: 01/28/2023] Open
Abstract
The integration of different sources of biological information about what defines a behavioral phenotype is difficult to unify in an entity that reflects the arithmetic sum of its individual parts. In this sense, the challenge of Systems Biology for understanding the “psychiatric phenotype” is to provide an improved vision of the shape of the phenotype as it is visualized by “Gestalt” psychology, whose fundamental axiom is that the observed phenotype (behavior or mental disorder) will be the result of the integrative composition of every part. Therefore, we propose the term “Gestaltomics” as a term from Systems Biology to integrate data coming from different sources of information (such as the genome, transcriptome, proteome, epigenome, metabolome, phenome, and microbiome). In addition to this biological complexity, the mind is integrated through multiple brain functions that receive and process complex information through channels and perception networks (i.e., sight, ear, smell, memory, and attention) that in turn are programmed by genes and influenced by environmental processes (epigenetic). Today, the approach of medical research in human diseases is to isolate one disease for study; however, the presence of an additional disease (co-morbidity) or more than one disease (multimorbidity) adds complexity to the study of these conditions. This review will present the challenge of integrating psychiatric disorders at different levels of information (Gestaltomics). The implications of increasing the level of complexity, for example, studying the co-morbidity with another disease such as cancer, will also be discussed.
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Affiliation(s)
| | - Osbaldo Resendis-Antonio
- Instituto Nacional de Medicina GenómicaMexico City, Mexico.,Human Systems Biology Laboratory, Coordinación de la Investigación Científica - Red de Apoyo a la Investigación, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, National Autonomous University of Mexico (UNAM)Mexico City, Mexico
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Cotton S, Azevedo R, Gaiteiro C, Ferreira D, Lima L, Peixoto A, Fernandes E, Neves M, Neves D, Amaro T, Cruz R, Tavares A, Rangel M, Silva AMN, Santos LL, Ferreira JA. Targeted O-glycoproteomics explored increased sialylation and identified MUC16 as a poor prognosis biomarker in advanced-stage bladder tumours. Mol Oncol 2017; 11:895-912. [PMID: 28156048 PMCID: PMC5537688 DOI: 10.1002/1878-0261.12035] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Revised: 01/24/2017] [Accepted: 01/24/2017] [Indexed: 12/30/2022] Open
Abstract
Bladder carcinogenesis and tumour progression is accompanied by profound alterations in protein glycosylation on the cell surface, which may be explored for improving disease management. In a search for prognosis biomarkers and novel therapeutic targets we have screened, using immunohistochemistry, a series of bladder tumours with differing clinicopathology for short-chain O-glycans commonly found in glycoproteins of human solid tumours. These included the Tn and T antigens and their sialylated counterparts sialyl-Tn(STn) and sialyl-T(ST), which are generally associated with poor prognosis. We have also explored the nature of T antigen sialylation, namely the sialyl-3-T(S3T) and sialyl-6-T(S6T) sialoforms, based on combinations of enzymatic treatments. We observed a predominance of sialoglycans over neutral glycoforms (Tn and T antigens) in bladder tumours. In particular, the STn antigen was associated with high-grade disease and muscle invasion, in accordance with our previous observations. The S3T and S6T antigens were detected for the first time in bladder tumours, but not in healthy urothelia, highlighting their cancer-specific nature. These glycans were also overexpressed in advanced lesions, especially in cases showing muscle invasion. Glycoproteomic analyses of advanced bladder tumours based on enzymatic treatments, Vicia villosa lectin-affinity chromatography enrichment and nanoLC-ESI-MS/MS analysis resulted in the identification of several key cancer-associated glycoproteins (MUC16, CD44, integrins) carrying altered glycosylation. Of particular interest were MUC16 STn+ -glycoforms, characteristic of ovarian cancers, which were found in a subset of advanced-stage bladder tumours facing the worst prognosis. In summary, significant alterations in the O-glycome and O-glycoproteome of bladder tumours hold promise for the development of novel noninvasive diagnostic tools and targeted therapeutics. Furthermore, abnormal MUC16 glycoforms hold potential as surrogate biomarkers of poor prognosis and unique molecular signatures for designing highly specific targeted therapeutics.
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Affiliation(s)
- Sofia Cotton
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, Porto, Portugal
| | - Rita Azevedo
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, Porto, Portugal.,Institute of Biomedical Sciences Abel Salazar, University of Porto, Portugal
| | - Cristiana Gaiteiro
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, Porto, Portugal
| | - Dylan Ferreira
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, Porto, Portugal
| | - Luís Lima
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, Porto, Portugal.,Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal
| | - Andreia Peixoto
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, Porto, Portugal.,Institute of Biomedical Sciences Abel Salazar, University of Porto, Portugal.,Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal
| | - Elisabete Fernandes
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, Porto, Portugal.,Institute of Biomedical Sciences Abel Salazar, University of Porto, Portugal.,Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal
| | - Manuel Neves
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, Porto, Portugal
| | - Diogo Neves
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, Porto, Portugal
| | - Teresina Amaro
- Department of Pathology, Hospital Pedro Hispano, Matosinhos, Portugal
| | - Ricardo Cruz
- Department of Urology, Portuguese Institute of Oncology of Porto, Portugal
| | - Ana Tavares
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, Porto, Portugal.,Department of Pathology, Portuguese Institute of Oncology of Porto, Portugal
| | - Maria Rangel
- UCIBIO-REQUIMTE, Instituto de Ciências Biomédicas Abel Salazar, University of Porto, Portugal
| | - André M N Silva
- UCIBIO-REQUIMTE/Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, Portugal
| | - Lúcio Lara Santos
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, Porto, Portugal.,Health School of University Fernando Pessoa, Porto, Portugal.,Department of Surgical Oncology, Portuguese Institute of Oncology, Porto, Portugal
| | - José Alexandre Ferreira
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology, Porto, Portugal.,Institute of Biomedical Sciences Abel Salazar, University of Porto, Portugal.,Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal.,Porto Comprehensive Cancer Center (P.ccc), Portugal
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48
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Discovering potential serological biomarker for chronic Hepatitis B Virus-related hepatocellular carcinoma in Chinese population by MAL-associated serum glycoproteomics analysis. Sci Rep 2017; 7:38918. [PMID: 28079114 PMCID: PMC5228127 DOI: 10.1038/srep38918] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 11/15/2016] [Indexed: 12/12/2022] Open
Abstract
The accuracy of current biomarkers for the diagnosis of hepatocellular carcinoma (HCC), especially chronic Hepatitis B Virus (HBV)-related HCC, is limited. Recent progress in glycoproteomics has provided a novel platform for screening novel serological biomarkers of HCC. In this study, lectin affinity chromatography by Maackia amurensis lectin (MAL) and iTRAQ combined with mass spectrometric analysis were performed to enrich and identify the glycoprotein fractions in serum samples from HBV-related HCC patients and from healthy controls. Seventeen differential MAL-associated glycoproteins were identified. Among them, Galectin 3 binding protein (Gal-3BP) was selected for further evaluated by ELISA analysis and showed a high diagnostic potential of HBV-related HCC, with the AUC of 0.898 and a sensitivity, specificity and accuracy of 80.00%, 93.75% and 86.88%, respectively. Moreover, we constructed a predictive model through the combined use of serum Gal-3BP and Alpha Fetoprotein (AFP), which improved the sensitivity (from 87.5% to 95%), specificity (from 93.75% to 95%) and accuracy (from 90.63% to 95%) of diagnosing early HCC. These data suggested serum Gal-3BP level is a promising biomarker to identify HBV-related HCC and the combined use of serum Gal-3BP and AFP improves the diagnostic potential of HBV-HCC compared with AFP alone in current clinical practice.
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Affiliation(s)
- Stefan Gaunitz
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Gabe Nagy
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Nicola L. B. Pohl
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Milos V. Novotny
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
- Regional Center for Applied Molecular Oncology, Masaryk Memorial Oncological Institute, 656 53 Brno, Czech Republic
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The Emerging Role of Proteomics in Precision Medicine: Applications in Neurodegenerative Diseases and Neurotrauma. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1007:59-70. [DOI: 10.1007/978-3-319-60733-7_4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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