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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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Li H, Peralta AG, Schoffelen S, Hansen AH, Arnsdorf J, Schinn SM, Skidmore J, Choudhury B, Paulchakrabarti M, Voldborg BG, Chiang AW, Lewis NE. LeGenD: determining N-glycoprofiles using an explainable AI-leveraged model with lectin profiling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.27.587044. [PMID: 38585977 PMCID: PMC10996628 DOI: 10.1101/2024.03.27.587044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Glycosylation affects many vital functions of organisms. Therefore, its surveillance is critical from basic science to biotechnology, including biopharmaceutical development and clinical diagnostics. However, conventional glycan structure analysis faces challenges with throughput and cost. Lectins offer an alternative approach for analyzing glycans, but they only provide glycan epitopes and not full glycan structure information. To overcome these limitations, we developed LeGenD, a lectin and AI-based approach to predict N-glycan structures and determine their relative abundance in purified proteins based on lectin-binding patterns. We trained the LeGenD model using 309 glycoprofiles from 10 recombinant proteins, produced in 30 glycoengineered CHO cell lines. Our approach accurately reconstructed experimentally-measured N-glycoprofiles of bovine Fetuin B and IgG from human sera. Explanatory AI analysis with SHapley Additive exPlanations (SHAP) helped identify the critical lectins for glycoprofile predictions. Our LeGenD approach thus presents an alternative approach for N-glycan analysis.
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Affiliation(s)
- Haining Li
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Angelo G. Peralta
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sanne Schoffelen
- National Biologics Facility Department of Biotechnology and Biomedicine, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs. Lyngby Denmark
| | - Anders Holmgaard Hansen
- National Biologics Facility Department of Biotechnology and Biomedicine, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs. Lyngby Denmark
| | - Johnny Arnsdorf
- National Biologics Facility Department of Biotechnology and Biomedicine, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs. Lyngby Denmark
| | - Song-Min Schinn
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jonathan Skidmore
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA
| | - Biswa Choudhury
- Glycobiology Research and Training Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Mousumi Paulchakrabarti
- Glycobiology Research and Training Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Bjorn G. Voldborg
- National Biologics Facility Department of Biotechnology and Biomedicine, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs. Lyngby Denmark
| | - Austin W.T. Chiang
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Nathan E. Lewis
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
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Guo Z, Tian C, Shi Y, Song XR, Yin W, Tao QQ, Liu J, Peng GP, Wu ZY, Wang YJ, Zhang ZX, Zhang J. Blood-based CNS regionally and neuronally enriched extracellular vesicles carrying pTau217 for Alzheimer's disease diagnosis and differential diagnosis. Acta Neuropathol Commun 2024; 12:38. [PMID: 38444036 PMCID: PMC10913681 DOI: 10.1186/s40478-024-01727-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 12/21/2023] [Indexed: 03/07/2024] Open
Abstract
Accurate differential diagnosis among various dementias is crucial for effective treatment of Alzheimer's disease (AD). The study began with searching for novel blood-based neuronal extracellular vesicles (EVs) that are more enriched in the brain regions vulnerable to AD development and progression. With extensive proteomic profiling, GABRD and GPR162 were identified as novel brain regionally enriched plasma EVs markers. The performance of GABRD and GPR162, along with the AD molecule pTau217, was tested using the self-developed and optimized nanoflow cytometry-based technology, which not only detected the positive ratio of EVs but also concurrently presented the corresponding particle size of the EVs, in discovery (n = 310) and validation (n = 213) cohorts. Plasma GABRD+- or GPR162+-carrying pTau217-EVs were significantly reduced in AD compared with healthy control (HC). Additionally, the size distribution of GABRD+- and GPR162+-carrying pTau217-EVs were significantly different between AD and non-AD dementia (NAD). An integrative model, combining age, the number and corresponding size of the distribution of GABRD+- or GPR162+-carrying pTau217-EVs, accurately and sensitively discriminated AD from HC [discovery cohort, area under the curve (AUC) = 0.96; validation cohort, AUC = 0.93] and effectively differentiated AD from NAD (discovery cohort, AUC = 0.91; validation cohort, AUC = 0.90). This study showed that brain regionally enriched neuronal EVs carrying pTau217 in plasma may serve as a robust diagnostic and differential diagnostic tool in both clinical practice and trials for AD.
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Affiliation(s)
- Zhen Guo
- Department of Pathology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, Zhejiang, China
| | - Chen Tian
- Department of Pathology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, Zhejiang, China
| | - Yang Shi
- Department of Pathology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, Zhejiang, China
- MOE Frontier Science Center for Brain Science and Brain-Machine Integration, School of Brain Science and Brain Medicine, Zhejiang University, Hangzhou, 310058, China
| | - Xue-Ru Song
- Department of Pathology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, Zhejiang, China
| | - Wei Yin
- Core Facilities, Zhejiang University School of Medicine, Hangzhou, 310011, China
| | - Qing-Qing Tao
- Department of Neurology and Research Center of Neurology in Second Affiliated Hospital, Key Laboratory of Medical Neurobiology of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, 310000, China
| | - Jie Liu
- Department of Neurology and Centre for Clinical Neuroscience, Daping Hospital, Third Military Medical University, Chongqing, 400042, China
| | - Guo-Ping Peng
- Department of Neurology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Zhi-Ying Wu
- Department of Neurology and Research Center of Neurology in Second Affiliated Hospital, Key Laboratory of Medical Neurobiology of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, 310000, China
| | - Yan-Jiang Wang
- Department of Neurology and Centre for Clinical Neuroscience, Daping Hospital, Third Military Medical University, Chongqing, 400042, China
| | - Zhen-Xin Zhang
- Department of Neurology and Clinical Epidemiology Unit, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Jing Zhang
- Department of Pathology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, Zhejiang, China.
- National Health and Disease Human Brain Tissue Resource Center, Zhejiang University, Hangzhou, 310012, China.
- Liangzhu Laboratory, Zhejiang University, 311121, Hangzhou, China.
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Wang S, Meng P, Yuan L, Guo X. Analysis of N-glycosylation protein of Kashin-Beck disease chondrocytes derived from induced pluripotent stem cells based on label-free strategies with LC-MS/MS. Mol Omics 2023; 19:454-463. [PMID: 37186116 DOI: 10.1039/d3mo00018d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
We aimed to compare N-glycosylation proteins in Kashin-Beck disease (KBD) chondrocytes and normal chondrocytes derived from induced pluripotent stem cells (iPSCs). KBD and normal iPSCs were reprogrammed from human KBD and normal dermal fibroblasts, respectively. Subsequently, chondrocytes were differentiated from KBD and normal iPSCs separately. Immunofluorescence was utilized to assay the protein markers of iPSCs and chondrocytes. Differential N-glycosylation proteins were screened using label-free strategies with LC-MS/MS. Bioinformatics analyses were utilized to interpret the functions of differential N-glycosylation proteins. Immunofluorescence staining revealed that both KBD-iPSCs and normal-iPSCs strongly expressed pluripotency markers OCT4 and NANOG. Meanwhile, chondrocyte markers collagen II and SOX9 are presented in KBD-iPSC-chondrocytes and normal-iPSC-chondrocytes. We obtained 87 differential N-glycosylation sites which corresponded to 68 differential proteins, which were constructed into 1 cluster. We obtained collagen type I trimer and 9 other biological processes; polysaccharide binding and 9 other molecular functions; regulation of transcription by RNA polymerase II and 9 other cellular components from GO; the Pl3K-Akt signaling pathway and 9 other KEGG pathways; peroxisome and 7 other subcellular locations; and integrin alpha chain, C-terminal cytoplasmic region, conserved site and 9 other classifications of domain annotations, and 2 networks. FGFR3 and LRP1 are expressed at higher levels in KBD-iPSC-chondrocytes, while the expressions of COL2A1, TIMP1, UNC5B, NOG, LEPR, and ITGA1 were down-regulated in KBD-iPSC-chondrocytes. The differential expressions of these N-glycosylation proteins may lead to the abnormal function of KBD chondrocytes.
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Affiliation(s)
- Sen Wang
- School of Public Health, Health Science Center, Xi'an Jiaotong University, Key Laboratory of Trace Elements and Endemic Diseases, National Health Commission, Xi'an, Shaanxi, China.
| | - Peilin Meng
- School of Public Health, Health Science Center, Xi'an Jiaotong University, Key Laboratory of Trace Elements and Endemic Diseases, National Health Commission, Xi'an, Shaanxi, China.
| | - Linlin Yuan
- School of Public Health, Health Science Center, Xi'an Jiaotong University, Key Laboratory of Trace Elements and Endemic Diseases, National Health Commission, Xi'an, Shaanxi, China.
| | - Xiong Guo
- School of Public Health, Health Science Center, Xi'an Jiaotong University, Key Laboratory of Trace Elements and Endemic Diseases, National Health Commission, Xi'an, Shaanxi, China.
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Wang D, Zhao Z, Xue X, Shi J, Shi W. Glycans in spent embryo culture medium are related to the implantation ability of blastocysts. Heliyon 2023; 9:e16255. [PMID: 37229168 PMCID: PMC10205493 DOI: 10.1016/j.heliyon.2023.e16255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 04/26/2023] [Accepted: 05/10/2023] [Indexed: 05/27/2023] Open
Abstract
Research question Does glycan profile in spent blastocyst culture medium have the potential to be used as a biomarker to predict implantation outcome. Design A nested case-control study was conducted in Northwest women's and children's Hospital, Xi'an, China. The patients underwent fresh IVF/ICSI cycles with single blastocyst transfer were included. Total 78 cases were included and separated into groups according to success (n = 39) and failure (n = 39) implantation outcomes. The glycosylation patterns in spent blastocyst culture medium were detected by lectin microarray containing 37 lectins using pooled samples and confirmed by reversed lectin microarray using individual sample. Results Binding signals of 10 lectins were found to be different between samples from successful and failed implantation. And 8 of them were confirmed that glycans binding to lectin NPA, UEA-I, MAL-I, LCA and GNA were significantly increased while DBA and BPL were decreased in the successful implantation compared to failed implantation. The glycan binding to lectin PHA-E + L had no difference between two groups. No significant differences in the glycan profile were found in spent culture medium of embryos with different morphological grades except the glycan binding to UEA-I between blastocysts of Poor and blastocysts of Medium. Conclusion Detection of glycan profile in spent culture medium may lead to a novel non-invasive assessment assay of embryo viability. In addition, these results may be helpful to further understanding molecular mechanisms in embryo implantation.
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Affiliation(s)
- Dongyang Wang
- Translational Medicine Center, Northwest Women and Children’s Hospital, No.1616 Yanxiang Road, Xi’an, Shaanxi, 710061, People’s Republic of China
- Assisted Reproduction Center, Northwest Women and Children’s Hospital, No.73 Houzaimen, Xi’an, Shaanxi, 710003, People’s Republic of China
| | - Zhenghao Zhao
- Assisted Reproduction Center, Northwest Women and Children’s Hospital, No.73 Houzaimen, Xi’an, Shaanxi, 710003, People’s Republic of China
| | - Xia Xue
- Assisted Reproduction Center, Northwest Women and Children’s Hospital, No.73 Houzaimen, Xi’an, Shaanxi, 710003, People’s Republic of China
| | - Juanzi Shi
- Translational Medicine Center, Northwest Women and Children’s Hospital, No.1616 Yanxiang Road, Xi’an, Shaanxi, 710061, People’s Republic of China
- Assisted Reproduction Center, Northwest Women and Children’s Hospital, No.73 Houzaimen, Xi’an, Shaanxi, 710003, People’s Republic of China
| | - Wenhao Shi
- Translational Medicine Center, Northwest Women and Children’s Hospital, No.1616 Yanxiang Road, Xi’an, Shaanxi, 710061, People’s Republic of China
- Assisted Reproduction Center, Northwest Women and Children’s Hospital, No.73 Houzaimen, Xi’an, Shaanxi, 710003, People’s Republic of China
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Zhao Y, Wang Y, Wu Y, Tao C, Xu R, Chen Y, Qian L, Xu T, Lian X. PKM2-mediated neuronal hyperglycolysis enhances the risk of Parkinson's disease in diabetic rats. J Pharm Anal 2023; 13:187-200. [PMID: 36908857 PMCID: PMC9999299 DOI: 10.1016/j.jpha.2022.11.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 11/15/2022] [Accepted: 11/16/2022] [Indexed: 11/23/2022] Open
Abstract
Epidemiological and animal studies indicate that pre-existing diabetes increases the risk of Parkinson's disease (PD). However, the mechanisms underlying this association remain unclear. In the present study, we found that high glucose (HG) levels in the cerebrospinal fluid (CSF) of diabetic rats might enhance the effect of a subthreshold dose of the neurotoxin 6-hydroxydopamine (6-OHDA) on the development of motor disorders, and the damage to the nigrostriatal dopaminergic neuronal pathway. In vitro, HG promoted the 6-OHDA-induced apoptosis in PC12 cells differentiated to neurons with nerve growth factor (NGF) (NGF-PC12). Metabolomics showed that HG promoted hyperglycolysis in neurons and impaired tricarboxylic acid cycle (TCA cycle) activity, which was closely related to abnormal mitochondrial fusion, thus resulting in mitochondrial loss. Interestingly, HG-induced upregulation of pyruvate kinase M2 (PKM2) combined with 6-OHDA exposure not only mediated glycolysis but also promoted abnormal mitochondrial fusion by upregulating the expression of MFN2 in NGF-PC12 cells. In addition, we found that PKM2 knockdown rescued the abnormal mitochondrial fusion and cell apoptosis induced by HG+6-OHDA. Furthermore, we found that shikonin (SK), an inhibitor of PKM2, restored the mitochondrial number, promoted TCA cycle activity, reversed hyperglycolysis, enhanced the tolerance of cultured neurons to 6-OHDA, and reduced the risk of PD in diabetic rats. Overall, our results indicate that diabetes promotes hyperglycolysis and abnormal mitochondrial fusion in neurons through the upregulation of PKM2, leading to an increase in the vulnerability of dopaminergic neurons to 6-OHDA. Thus, the inhibition of PKM2 and restoration of mitochondrial metabolic homeostasis/pathways may prevent the occurrence and development of diabetic PD.
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Affiliation(s)
- Ya Zhao
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yanwei Wang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yuying Wu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Cimin Tao
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Rui Xu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yong Chen
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Linghui Qian
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Tengfei Xu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Xiaoyuan Lian
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
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A combination of surface-initiated atom transfer radical polymerization and photo-initiated "thiol-ene" click chemistry: Fabrication of functionalized macroporous adsorption resins for enrichment of glycopeptides. J Chromatogr A 2023; 1689:463774. [PMID: 36630850 DOI: 10.1016/j.chroma.2023.463774] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 01/02/2023] [Accepted: 01/03/2023] [Indexed: 01/06/2023]
Abstract
A hydrophilic adsorbent (Cys@poly(AMA)@MAR) was successfully prepared for the enrichment of N-glycopeptides via surface-initiated atom transfer radical polymerization (SI-ATRP) and photo-initiated "thiol-ene" reaction using monodisperse macroporous adsorbent resin (MAR) as adsorption matrix. Due to the presence of electron-deficient acrylic groups and electron-rich vinyl groups in allyl methacrylate (AMA), both of them can participate in free radical reaction. Therefore, the polymerization time of SI-ATRP was optimized. The resulting poly(AMA)@MAR was modified with l-cysteine (L-Cys) via photo-initiated "thiol-ene" reaction, and the amount of vinyl retained was determined by measuring the adsorption of Cu2+. The Cys@poly(AMA)@MAR pendant brushes with high density of amine and carboxyl groups could capture N-glycopeptides from IgG digest and human serum digest by hydrophilic interaction. The 22 N-glycopeptides were identified from IgG digest and the limit of detection reached 10 fmol. The 319 N-glycosylation sites and 583 N-glycopeptides were identified from 2 μL human serum digest and mapped to 147 glycoproteins. It demonstrates great potential and commercialization prospects for the enrichment of N-glycopeptides.
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Effects of the genetic knockout of the β-1,3-galactosyltransferase 2 on spatial learning and neurons in the adult mouse hippocampus and somatosensory cortex. Neuroreport 2023; 34:46-55. [PMID: 36504040 DOI: 10.1097/wnr.0000000000001857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
OBJECTIVE Glycosyltransferases contribute to the biosynthesis of glycoproteins, proteoglycans and glycolipids and play essential roles in various processes in the brain, such as learning and memory, brain development, neuronal survival and neurodegeneration. β-1,3-galactosyltransferase 2 (B3galt2) belongs to the β-1,3-galactosyltransferase gene family and is highly expressed in the brain. Recent studies have indicated that B3galt2 plays a vital role in ischemic stroke through several signaling pathways in a mouse model. However, the function of B3galt2 in the brain remains poorly understood. METHODS The genotypes of mice were determined by PCR. To verify B3galt2 expression in an adult mouse brain, X-gal staining was performed in 6-month-old B3galt2 heterozygous (B3galt2+/-) mice. Using adult B3galt2 homozygous (B3galt2-/-), heterozygous and wild-type (WT) littermates, spatial learning and memory were determined by the Morris Water Maze test, and neurotoxicity and synaptic plasticity were examined by immunofluorescence. RESULTS B3galt2 was highly expressed in the adult mouse hippocampus and cortex, especially in the hippocampal dentate gyrus. Compared to that of WT mice, the spatial learning ability of adult B3galt2-/- mice was impaired. B3galt2 mutations also caused neuronal loss and synaptic dysfunction in the hippocampus and somatosensory cortex, and these changes were more obvious in B3galt2-/- mice than in B3galt2+/- mice. CONCLUSIONS The findings indicate that B3galt2 plays an important role in cognitive function, neuronal maintenance and synaptic plasticity in the adult mouse brain. This study suggests that genetic and/or pharmacological manipulation of glycosyltransferases may be a novel strategy for elucidating the mechanism of and managing various brain disorders.
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Mahara G, Tian C, Xu X, Zhu J. Breakthrough of glycobiology in the 21st century. Front Immunol 2023. [DOI: doi 10.3389/fimmu.2022.1071360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
As modern medicine began to emerge at the turn of the 20th century, glycan-based therapies advanced. DNA- and protein-centered therapies became widely available. The research and development of structurally defined carbohydrates have led to new tools and methods that have sparked interest in the therapeutic applications of glycans. One of the latest omics disciplines to emerge in the contemporary post-genomics age is glycomics. In addition, to providing hope for patients and people with different health conditions through a deeper understanding of the mechanisms of common complex diseases, this new specialty in system sciences has much to offer to communities involved in the development of diagnostics and therapeutics in medicine and life sciences.This review focuses on recent developments that have pushed glycan-based therapies into the spotlight in medicine and the technologies powering these initiatives, which we can take as the most significant success of the 21st century.
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Peng W, Kobeissy F, Mondello S, Barsa C, Mechref Y. MS-based glycomics: An analytical tool to assess nervous system diseases. Front Neurosci 2022; 16:1000179. [PMID: 36408389 PMCID: PMC9671362 DOI: 10.3389/fnins.2022.1000179] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 10/05/2022] [Indexed: 08/27/2023] Open
Abstract
Neurological diseases affect millions of peopleochemistryorldwide and are continuously increasing due to the globe's aging population. Such diseases affect the nervous system and are characterized by a progressive decline in brain function and progressive cognitive impairment, decreasing the quality of life for those with the disease as well as for their families and loved ones. The increased burden of nervous system diseases demands a deeper insight into the biomolecular mechanisms at work during disease development in order to improve clinical diagnosis and drug design. Recently, evidence has related glycosylation to nervous system diseases. Glycosylation is a vital post-translational modification that mediates many biological functions, and aberrant glycosylation has been associated with a variety of diseases. Thus, the investigation of glycosylation in neurological diseases could provide novel biomarkers and information for disease pathology. During the last decades, many techniques have been developed for facilitation of reliable and efficient glycomic analysis. Among these, mass spectrometry (MS) is considered the most powerful tool for glycan analysis due to its high resolution, high sensitivity, and the ability to acquire adequate structural information for glycan identification. Along with MS, a variety of approaches and strategies are employed to enhance the MS-based identification and quantitation of glycans in neurological samples. Here, we review the advanced glycomic tools used in nervous system disease studies, including separation techniques prior to MS, fragmentation techniques in MS, and corresponding strategies. The glycan markers in common clinical nervous system diseases discovered by utilizing such MS-based glycomic tools are also summarized and discussed.
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Affiliation(s)
- Wenjing Peng
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, United States
| | - Firas Kobeissy
- Program for Neurotrauma, Neuroproteomics and Biomarkers Research, Department of Emergency Medicine, University of Florida, Gainesville, FL, United States
| | - Stefania Mondello
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Messina, Italy
| | - Chloe Barsa
- Program for Neurotrauma, Neuroproteomics and Biomarkers Research, Department of Emergency Medicine, University of Florida, Gainesville, FL, United States
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, United States
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Chang D, Zaia J. Methods to improve quantitative glycoprotein coverage from bottom-up LC-MS data. MASS SPECTROMETRY REVIEWS 2022; 41:922-937. [PMID: 33764573 DOI: 10.1002/mas.21692] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 12/24/2020] [Accepted: 03/11/2021] [Indexed: 05/18/2023]
Abstract
Advances in mass spectrometry instrumentation, methods development, and bioinformatics have greatly improved the ease and accuracy of site-specific, quantitative glycoproteomics analysis. Data-dependent acquisition is the most popular method for identification and quantification of glycopeptides; however, complete coverage of glycosylation site glycoforms remains elusive with this method. Targeted acquisition methods improve the precision and accuracy of quantification, but at the cost of throughput and discoverability. Data-independent acquisition (DIA) holds great promise for more complete and highly quantitative site-specific glycoproteomics analysis, while maintaining the ability to discover novel glycopeptides without prior knowledge. We review additional features that can be used to increase selectivity and coverage to the DIA workflow: retention time modeling, which would simplify the interpretation of complex tandem mass spectra, and ion mobility separation, which would maximize the sampling of all precursors at a giving chromatographic retention time. The instrumentation and bioinformatics to incorporate these features into glycoproteomics analysis exist. These improvements in quantitative, site-specific analysis will enable researchers to assess glycosylation similarity in related biological systems, answering new questions about the interplay between glycosylation state and biological function.
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Affiliation(s)
- Deborah Chang
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Joseph Zaia
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts, USA
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Zhai B, Xie S, Peng J, Qiu Y, Liu Y, Zhu X, He J, Zhang J. Glycosylation Analysis of Feline Small Intestine Following Toxoplasma gondii Infection. Animals (Basel) 2022; 12:ani12202858. [PMID: 36290246 PMCID: PMC9597833 DOI: 10.3390/ani12202858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 10/12/2022] [Accepted: 10/17/2022] [Indexed: 12/01/2022] Open
Abstract
Simple Summary Toxoplasma gondii has a serious impact on public health and the economic development of animal husbandry. Glycosylation, especially N-glycosylation, the pattern modification of proteins, is closely related to the biological functions of proteins, and our study used it to analyze glycosylation alterations in the small intestine of cats infected with T. gondii. The results of the present study showed that 56 glycosylated peptides were upregulated and 37 glycosylated peptides were downregulated. Additionally, we also identified eight N-glycosylated proteins of T. gondii including eight N-glycopeptides and eight N-glycosylation sites. Moreover, the protein eEF2 and its corresponding peptide sequence were identified, with GO terms (i.e., cellular process and metabolic process, cell and cell part, and catalytic activity) that were significantly enriched in the T. gondii MAPK pathway. In addition, the Clusters of Orthologous Groups of proteins (COG) function prediction results showed that posttranslational modification, protein turnover, and chaperones (11%) had the highest enrichment for T. gondii. The host proteins ICAM-1 and PPT1 and the endoplasmic reticulum stress pathway may play an important role in the glycosylation of T. gondii-infected hosts. Our study may provide a new target for T. gondii detection to prevent the spread of T. gondii oocysts in the future. Abstract Toxoplasma gondii (T. gondii) is responsible for severe human and livestock diseases, huge economic losses, and adversely affects the health of the public and the development of animal husbandry. Glycosylation is a common posttranslational modification of proteins in eukaryotes, and N-glycosylation is closely related to the biological functions of proteins. However, glycosylation alterations in the feline small intestine following T. gondii infection have not been reported. In this study, the experimental group was intragastrically challenged with 600 brain cysts of the Prugniuad (Pru) strain that were collected from infected mice. The cats’ intestinal epithelial tissues were harvested at 10 days post-infection and then sent for protein glycosylation analysis. High-performance liquid chromatography coupled to tandem mass spectrometry was used to analyze the glycosylation alterations in the small intestine of cats infected with T. gondii. The results of the present study showed that 56 glycosylated peptides were upregulated and 37 glycosylated peptides were downregulated in the feline small intestine infected by T. gondii. Additionally, we also identified eight N-glycosylated proteins of T. gondii including eight N-glycopeptides and eight N-glycosylation sites. The protein A0A086JND6_TOXGO (eEF2) and its corresponding peptide sequence were identified in T. gondii infection. Some special GO terms (i.e., cellular process and metabolic process, cell and cell part, and catalytic activity) were significantly enriched, and the Clusters of Orthologous Groups of proteins (COG) function prediction results showed that posttranslational modification, protein turnover, and chaperones (11%) had the highest enrichment for T. gondii. Interestingly, eEF2, a protein of T. gondii, is also involved in the significantly enriched T. gondii MAPK pathway. The host proteins ICAM-1 and PPT1 and the endoplasmic reticulum stress pathway may play an important role in the glycosylation of Toxoplasma-infected hosts. This is the first report showing that T. gondii oocysts can undergo N-glycosylation in the definitive host and that eEF2 is involved, which may provide a new target for T. gondii detection to prevent the spread of T. gondii oocysts in the future.
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Affiliation(s)
- Bintao Zhai
- Key Laboratory of Veterinary Pharmaceutical Development, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Lanzhou 730050, China
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China
| | - Shichen Xie
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong 030801, China
- Research Center for Parasites & Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, China
| | - Junjie Peng
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China
| | - Yanhua Qiu
- Key Laboratory of Veterinary Pharmaceutical Development, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Lanzhou 730050, China
- College of Veterinary Medicine, Northwest A&F University, Xianyang 712100, China
| | - Yang Liu
- College of Life Science, Ningxia University, Yinchuan 750021, China
| | - Xingquan Zhu
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong 030801, China
- Research Center for Parasites & Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, China
- Key Laboratory of Veterinary Public Health of Yunnan Province, College of Veterinary Medicine, Yunnan Agricultural University, Kunming 650201, China
| | - Junjun He
- Key Laboratory of Veterinary Public Health of Yunnan Province, College of Veterinary Medicine, Yunnan Agricultural University, Kunming 650201, China
- Correspondence: (J.H.); (J.Z.)
| | - Jiyu Zhang
- Key Laboratory of Veterinary Pharmaceutical Development, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Lanzhou 730050, China
- Correspondence: (J.H.); (J.Z.)
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13
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Zhou S, Liu D, Chen J, Xiang C, Xiang J, Yang M. Electrochemical Quantitation of the Glycosylation Level of Serum Neurofilament Light Chain for the Diagnosis of Neurodegeneration: An Interface-Solution Dual-Path Amplification Strategy. Anal Chem 2022; 94:11433-11440. [PMID: 35913270 DOI: 10.1021/acs.analchem.2c02753] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Serum neurofilament light chain (NFL), a potential general biomarker for neurodegenerative diseases, is not specific enough to differentiate neurodegenerative diseases from other brain diseases such as cerebral thrombosis (CT). According to the importance of glycosylation in neurodegenerative pathogenesis, the NFL glycosylation level (oNFL/tNFL), defined as the ratio of glycosylated NFL (oNFL) to total NFL (tNFL), may be a more effective index. The major challenge in serum oNFL/tNFL detection is the ultra-low abundance of both NFL forms. In this paper, we achieved a convenient one-step electrochemical quantitation of oNFL/tNFL based on an interface-solution dual-path amplification strategy. Two amplified electrochemical signals─the reduction of Cu2+ from adsorbed porous nanoparticles on the sensor interface and the reduction of O2 from horseradish peroxidase-catalyzed H2O2 disproportionation in solution─were adopted to quantify tNFL and oNFL, respectively. The electrochemical sensor displayed good sensitivity, selectivity, and reproducibility. The dynamic range is 1-25 pg mL-1 for tNFL and 0.25-25 pg mL-1 for oNFL, respectively. By analyzing the clinic serum samples, for the first time, our work provided the abundance of oNFL in human serum and revealed that the oNFL/tNFL is effective not only in differentiating three kinds of brain damage patients from healthy people but also in differentiating neurodegeneration from non-neurodegeneration CT patients. As a general biomarker, the oNFL/tNFL is more specific than NFL, which is hoped to be a new and valid indicator for the diagnosis, progression, prediction, and treatment evaluation of neurodegenerative diseases.
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Affiliation(s)
- Siqiuyue Zhou
- Hunan Provincial Key Laboratory of Micro & Nano Materials Interface Science, College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, P. R. China.,National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Central South University, Changsha 410083, P. R. China
| | - Dan Liu
- Eye Center of Xiangya Hospital, Central South University, Changsha 410083, P. R. China
| | - Jia Chen
- Hunan Provincial Key Laboratory of Micro & Nano Materials Interface Science, College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, P. R. China
| | - Chao Xiang
- Wuhan Red Cross Hospital, Wuhan 430015, P. R. China
| | - Juan Xiang
- Hunan Provincial Key Laboratory of Micro & Nano Materials Interface Science, College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, P. R. China.,National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Central South University, Changsha 410083, P. R. China
| | - Minghui Yang
- Hunan Provincial Key Laboratory of Micro & Nano Materials Interface Science, College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, P. R. China
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14
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Tian C, Stewart T, Hong Z, Guo Z, Aro P, Soltys D, Pan C, Peskind ER, Zabetian CP, Shaw LM, Galasko D, Quinn JF, Shi M, Zhang J. Blood extracellular vesicles carrying synaptic function- and brain-related proteins as potential biomarkers for Alzheimer's disease. Alzheimers Dement 2022; 19:10.1002/alz.12723. [PMID: 35779041 PMCID: PMC9806186 DOI: 10.1002/alz.12723] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 05/18/2022] [Accepted: 05/19/2022] [Indexed: 01/04/2023]
Abstract
INTRODUCTION Objective and accessible markers for Alzheimer's disease (AD) and other dementias are critically needed. METHODS We identified NMDAR2A, a protein related to synaptic function, as a novel marker of central nervous system (CNS)-derived plasma extracellular vesicles (EVs) and developed a flow cytometry-based technology for detecting such plasma EVs readily. The assay was initially tested in our local cross-sectional study to distinguish AD patients from healthy controls (HCs) or from Parkinson's disease (PD) patients, followed by a validation study using an independent cohort collected from multiple medical centers (the Alzheimer's Disease Neuroimaging Initiative). Cerebrospinal fluid AD molecular signature was used to confirm diagnoses of all AD participants. RESULTS Likely CNS-derived EVs in plasma were significantly reduced in AD compared to HCs in both cohorts. Integrative models including CNS-derived EV markers and AD markers present on EVs reached area under the curve of 0.915 in discovery cohort and 0.810 in validation cohort. DISCUSSION This study demonstrated that robust and rapid analysis of individual neuron-derived synaptic function-related EVs in peripheral blood may serve as a helpful marker of synaptic dysfunction in AD and dementia.
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Affiliation(s)
- Chen Tian
- Department of Pathology, First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang, Hangzhou, China
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, USA
| | - Tessandra Stewart
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, USA
| | - Zhen Hong
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, USA
- Department of Neurology, West China Medical School, Sichuan University, Chengdu, Sichuan, China
| | - Zhen Guo
- Department of Pathology, First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang, Hangzhou, China
| | - Patrick Aro
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, USA
| | - David Soltys
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, USA
| | - Catherine Pan
- Department of Pathology, First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang, Hangzhou, China
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, USA
| | - Elaine R Peskind
- Department of Psychiatry and Behavioral Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Northwest (VISN-20) Mental Illness, Research, Education, and Clinical Center, Veterans Affairs Puget Sound Health Care System, Seattle, WA, USA
| | - Cyrus P. Zabetian
- Veterans Affairs Puget Sound Health Care System, Seattle, WA, USA
- Department of Neurology, University of Washington School of Medicine, Seattle, WA, USA
| | - Leslie M. Shaw
- Center for Neurodegenerative Disease Research, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Douglas Galasko
- Department of Neurology, University of California, San Diego, California, USA
| | - Joseph F Quinn
- Department of Neurology, Oregon Health & Science University, Portland, OR, USA
- Department of Neurology and Parkinson’s Disease Research Education and Clinical Care Center (PADRECC), VA Portland Healthcare System, Portland, OR, USA
| | - Min Shi
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, USA
| | - Jing Zhang
- Department of Pathology, First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang, Hangzhou, China
- National Health and Disease Human Brain Tissue Resource Center, Zhejiang University, Zhejiang, Hangzhou, China
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15
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Lyu Y, Deng H, Qu C, Qiao L, Liu X, Xiao X, Liu J, Guo Z, Zhao Y, Han J, Lammi MJ. Identification of proteins and N-glycosylation sites of knee cartilage in Kashin-Beck disease compared with osteoarthritis. Int J Biol Macromol 2022; 210:128-138. [PMID: 35526762 DOI: 10.1016/j.ijbiomac.2022.05.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 05/02/2022] [Indexed: 11/18/2022]
Abstract
The aim of this study was to identify crucial proteins and N-glycosylated sites in the pathological mechanism of Kashin-Beck disease (KBD) compared with osteoarthritis (OA). Nine KBD knee subjects and nine OA knee subjects were selected for the study. Quantitative proteomics and N-glycoproteomics data of KBD and OA were obtained by protein and N-glycoprotein enrichment and LC-MS/MS analysis. Differentially expressed proteins or N-glycosylation sites were examined with a comparative analysis between KBD and OA. Total 2205 proteins were identified in proteomic analysis, of which 375 were significantly different. Among these, 121 proteins were up-regulated and 254 were down-regulated. In N-glycoproteomic analysis, 278 different N-glycosylated sites that were related to 187 N-glycoproteins were identified. Proteins and their N-glycosylated sites are associated with KBD pathological process including ITGB1, LRP1, ANO6, COL1A1, MXRA5, DPP4, and CSPG4. CRLF1 and GLG1 are proposed to associate with both KBD and OA pathological processes. Key pathways in KBD vs. OA proteomic and N-glycoproteomic analysis contained extracellular matrix receptor interaction, focal adhesion, phagosome, protein digestion, and absorption. N-glycosylation may influence the pathological process by affecting the integrity of chondrocytes or cartilage. It regulated the intercellular signal transduction pathway, which contributes to cartilage destruction in KBD.
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Affiliation(s)
- Yizhen Lyu
- School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, Shaanxi, People's Republic of China
| | - Huan Deng
- School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, Shaanxi, People's Republic of China
| | - Chengjuan Qu
- Department of Odontology, Umeå University, Umeå 90185, Sweden
| | - Lichun Qiao
- School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, Shaanxi, People's Republic of China
| | - Xuan Liu
- School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, Shaanxi, People's Republic of China
| | - Xiang Xiao
- School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, Shaanxi, People's Republic of China
| | - Jiaxin Liu
- School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, Shaanxi, People's Republic of China
| | - Ziwei Guo
- School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, Shaanxi, People's Republic of China
| | - Yan Zhao
- School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, Shaanxi, People's Republic of China
| | - Jing Han
- School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, Shaanxi, People's Republic of China.
| | - Mikko J Lammi
- School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, Shaanxi, People's Republic of China; Department of Integrative Medical Biology, Umeå University, Umeå 90187, Sweden
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16
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Feng Y, Jiang H, Li G, He G, Li X. Decreased Expression of Protein O-linked Mannose β 1,2-N-Acetylglucosaminyltransferase 1 Contributes to Alzheimer's Disease-like Pathologies. J Neurophysiol 2022; 127:1067-1074. [PMID: 35320023 DOI: 10.1152/jn.00362.2021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Alzheimer's disease (AD) is pathologically characterized by senile plaques and neurofibrillary tangles composed of β-amyloid peptide (Aβ) and tau hyperphosphorylation, respectively. Mannosylation, a particular type of post-translational modification, may be involved in the pathogenesis of AD. However, its underlying mechanism remains unclear. Protein O-linked mannose β 1,2-N-acetylglucosaminyltransferase 1 (POMGnT1) catalyzes the formation of the N-acetylglucosamine β-1,2-Man linkage of O-mannosylglycan, which can increase the protein post-translational mannosylation level. The defective POMGnT1 gene leads to the hypomannosylation of proteins, which may cause cognitive decline in aged people. This study aimed to investigate whether POMGnT1 participated in the pathogenesis of AD and explore its underlying role using AD mouse and cell models. In this study, the expression of POMGnT1 was measured in AD models [β-amyloid precursor protein (APP)/presenilin-1 (PS1) transgenic mice, an AD mouse model; N2a cells stably transfected with Swedish mutant APP (N2a/APP), an AD cell model]. The results revealed that the expression of POMGnT1 decreased in AD mouse and cell models. Additionally, POMGnT1-overexpressing N2a/APP cells were built by retroviral transfection. POMGnT1 overexpression may lower Aβ levels by reducing APP production and downregulating β-and γ-secretase activities. It also promoted clearance of Aβ by upregulating insulin-degrading enzymes and ameliorated tau hyperphosphorylation. Hence, it was concluded that POMGnT1 was involved in the pathogenic process of AD. The decreased expression of POMGnT1 contributes to AD-like pathologies.
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Affiliation(s)
- Yuxue Feng
- Department of Neurology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Hanxiao Jiang
- Department of Neurology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Gongbo Li
- Department of Neurology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Guiqiong He
- Institute of Neuroscience, Chongqing Medical University, Chongqing, China
| | - Xiaofeng Li
- Department of Neurology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
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17
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Yang J, Yin M, Hou Y, Li H, Guo Y, Yu H, Zhang K, Zhang C, Jia L, Zhang F, Li X, Bian H, Li Z. Role of ammonia for brain abnormal protein glycosylation during the development of hepatitis B virus-related liver diseases. Cell Biosci 2022; 12:16. [PMID: 35164881 PMCID: PMC8842931 DOI: 10.1186/s13578-022-00751-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 01/29/2022] [Indexed: 11/30/2022] Open
Abstract
Background Ammonia is the most typical neurotoxin in hepatic encephalopathy (HE), but the underlying pathophysiology between ammonia and aberrant glycosylation in HE remains unknown. Results Here, we used HBV transgenic mice and astrocytes to present a systems-based study of glycosylation changes and corresponding enzymes associated with the key factors of ammonia in HE. We surveyed protein glycosylation changes associated with the brain of HBV transgenic mice by lectin microarrays. Upregulation of Galβ1-3GalNAc mediated by core 1 β1,3-galactosyltransferase (C1GALT1) was identified as a result of ammonia stimulation. Using in vitro assays, we validated that upregulation of C1GALT1 is a driver of deregulates calcium (Ca2+) homeostasis by overexpression of inositol 1,4,5-trisphosphate receptor type 1 (IP3R1) in astrocytes. Conclusions We demonstrated that silencing C1GALT1 could depress the IP3R1 expression, an effective strategy to inhibit the ammonia-induced upregulation of Ca2+ activity, thereby C1GALT1 and IP3R1 may serve as therapeutic targets in hyperammonemia of HE. Supplementary Information The online version contains supplementary material available at 10.1186/s13578-022-00751-4.
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Affiliation(s)
- Jiajun Yang
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Mengqi Yin
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Yao Hou
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Hao Li
- Cell Engineering Research Centre and Department of Cell Biology, Fourth Military Medical University, Xi'an, 710032, China
| | - Yonghong Guo
- Department of Infectious Diseases, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710004, China
| | - Hanjie Yu
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Kun Zhang
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Chen Zhang
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Liyuan Jia
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Fan Zhang
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Xia Li
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Huijie Bian
- Cell Engineering Research Centre and Department of Cell Biology, Fourth Military Medical University, Xi'an, 710032, China.
| | - Zheng Li
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, 710069, China.
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18
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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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Mahara G, Tian C, Xu X, Zhu J. Breakthrough of glycobiology in the 21st century. Front Immunol 2022; 13:1071360. [PMID: 36685548 PMCID: PMC9850147 DOI: 10.3389/fimmu.2022.1071360] [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: 10/16/2022] [Accepted: 12/01/2022] [Indexed: 01/07/2023] Open
Abstract
As modern medicine began to emerge at the turn of the 20th century, glycan-based therapies advanced. DNA- and protein-centered therapies became widely available. The research and development of structurally defined carbohydrates have led to new tools and methods that have sparked interest in the therapeutic applications of glycans. One of the latest omics disciplines to emerge in the contemporary post-genomics age is glycomics. In addition, to providing hope for patients and people with different health conditions through a deeper understanding of the mechanisms of common complex diseases, this new specialty in system sciences has much to offer to communities involved in the development of diagnostics and therapeutics in medicine and life sciences.This review focuses on recent developments that have pushed glycan-based therapies into the spotlight in medicine and the technologies powering these initiatives, which we can take as the most significant success of the 21st century.
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Affiliation(s)
- Gehendra Mahara
- Clinical Research Center, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
- Department of Cardiovascular Medicine, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Cuihong Tian
- Clinical Research Center, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
- Department of Cardiovascular Medicine, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
- Center for Precision Health, Edith Cowan University, Perth, WA, Australia
| | - Xiaojia Xu
- Clinical Research Center, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
- Center for Precision Health, Edith Cowan University, Perth, WA, Australia
- Department of Infection Control, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Jinxiu Zhu
- Institute of Clinical Electrocardiography, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
- Longgang Maternity and Child Institute of Shantou University Medical College, Shenzhen, Guangdong, China
- *Correspondence: Jinxiu Zhu,
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20
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Cline EN, Alvarez C, Duan J, Patrie SM. Online μSEC 2-nRPLC-MS for Improved Sensitivity of Intact Protein Detection of IEF-Separated Nonhuman Primate Cerebrospinal Fluid Proteins. Anal Chem 2021; 93:16741-16750. [PMID: 34881887 PMCID: PMC10476446 DOI: 10.1021/acs.analchem.1c00396] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Proteoform-resolved information, obtained by top-down (TD) "intact protein" proteomics, is expected to contribute substantially to the understanding of molecular pathogenic mechanisms and, in turn, identify novel therapeutic and diagnostic targets. However, the robustness of mass spectrometry (MS) analysis of intact proteins in complex biological samples is hindered by the high dynamic range in protein concentration and mass, protein instability, and buffer complexity. Here, we describe an evolutionary step for intact protein investigations through the online implementation of tandem microflow size-exclusion chromatography with nanoflow reversed-phase liquid chromatography and MS (μSEC2-nRPLC-MS). Online serial high-/low-pass SEC filtration overcomes the aforementioned hurdles to intact proteomic analysis through automated sample desalting/cleanup and enrichment of target mass ranges (5-155 kDa) prior to nRPLC-MS. The coupling of μSEC to nRPLC is achieved through a novel injection volume control (IVC) strategy of inserting protein trap columns, pre- and post-μSEC columns, to enable injection of dilute samples in high volumes without loss of sensitivity or resolution. Critical characteristics of the approach are tested via rigorous investigations on samples of varied complexity and chemical background. Application of the platform to cerebrospinal fluid (CSF) prefractionated by OFFGEL isoelectric focusing drastically increases the number of intact mass tags (IMTs) detected within the target mass range (5-30 kDa) in comparison to one-dimensional nRPLC-MS with approximately 100× less CSF than previous OFFGEL studies. Furthermore, the modular design of the μSEC2-nRPLC-MS platform is robust and promises significant flexibility for large-scale TDMS analysis of diverse samples either directly or in concert with other multidimensional fractionation steps.
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Affiliation(s)
- Erika N Cline
- Department of Chemistry and the Proteomics Center of Excellence, Northwestern University, 2145 Sheridan Rd, Evanston, Illinois 60208, United States
| | - Carina Alvarez
- Department of Chemistry and the Proteomics Center of Excellence, Northwestern University, 2145 Sheridan Rd, Evanston, Illinois 60208, United States
| | - Jiana Duan
- Department of Chemistry and the Proteomics Center of Excellence, Northwestern University, 2145 Sheridan Rd, Evanston, Illinois 60208, United States
| | - Steven M Patrie
- Department of Chemistry and the Proteomics Center of Excellence, Northwestern University, 2145 Sheridan Rd, Evanston, Illinois 60208, United States
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21
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Hasan MM, Mimi MA, Mamun MA, Islam A, Waliullah ASM, Nabi MM, Tamannaa Z, Kahyo T, Setou M. Mass Spectrometry Imaging for Glycome in the Brain. Front Neuroanat 2021; 15:711955. [PMID: 34393728 PMCID: PMC8358800 DOI: 10.3389/fnana.2021.711955] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 07/07/2021] [Indexed: 12/12/2022] Open
Abstract
Glycans are diverse structured biomolecules that play crucial roles in various biological processes. Glycosylation, an enzymatic system through which various glycans are bound to proteins and lipids, is the most common and functionally crucial post-translational modification process. It is known to be associated with brain development, signal transduction, molecular trafficking, neurodegenerative disorders, psychopathologies, and brain cancers. Glycans in glycoproteins and glycolipids expressed in brain cells are involved in neuronal development, biological processes, and central nervous system maintenance. The composition and expression of glycans are known to change during those physiological processes. Therefore, imaging of glycans and the glycoconjugates in the brain regions has become a “hot” topic nowadays. Imaging techniques using lectins, antibodies, and chemical reporters are traditionally used for glycan detection. However, those techniques offer limited glycome detection. Mass spectrometry imaging (MSI) is an evolving field that combines mass spectrometry with histology allowing spatial and label-free visualization of molecules in the brain. In the last decades, several studies have employed MSI for glycome imaging in brain tissues. The current state of MSI uses on-tissue enzymatic digestion or chemical reaction to facilitate successful glycome imaging. Here, we reviewed the available literature that applied MSI techniques for glycome visualization and characterization in the brain. We also described the general methodologies for glycome MSI and discussed its potential use in the three-dimensional MSI in the brain.
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Affiliation(s)
- Md Mahmudul Hasan
- Department of Cellular & Molecular Anatomy, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Mst Afsana Mimi
- Department of Cellular & Molecular Anatomy, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Md Al Mamun
- Department of Cellular & Molecular Anatomy, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Ariful Islam
- Department of Cellular & Molecular Anatomy, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - A S M Waliullah
- Department of Cellular & Molecular Anatomy, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Md Mahamodun Nabi
- Department of Cellular & Molecular Anatomy, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Zinat Tamannaa
- Department of Cellular & Molecular Anatomy, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Tomoaki Kahyo
- Department of Cellular & Molecular Anatomy, Hamamatsu University School of Medicine, Hamamatsu, Japan.,International Mass Imaging Center, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Mitsutoshi Setou
- Department of Cellular & Molecular Anatomy, Hamamatsu University School of Medicine, Hamamatsu, Japan.,International Mass Imaging Center, Hamamatsu University School of Medicine, Hamamatsu, Japan.,Department of Systems Molecular Anatomy, Institute for Medical Photonics Research, Preeminent Medical Photonics Education & Research Center, Hamamatsu, Japan
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22
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N-Glycomics of Human Erythrocytes. Int J Mol Sci 2021; 22:ijms22158063. [PMID: 34360826 PMCID: PMC8347577 DOI: 10.3390/ijms22158063] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 07/22/2021] [Accepted: 07/26/2021] [Indexed: 12/29/2022] Open
Abstract
Glycosylation is a complex post-translational modification that conveys functional diversity to glycoconjugates. Cell surface glycosylation mediates several biological activities such as induction of the intracellular signaling pathway and pathogen recognition. Red blood cell (RBC) membrane N-glycans determine blood type and influence cell lifespan. Although several proteomic studies have been carried out, the glycosylation of RBC membrane proteins has not been systematically investigated. This work aims at exploring the human RBC N-glycome by high-sensitivity MALDI-MS techniques to outline a fingerprint of RBC N-glycans. To this purpose, the MALDI-TOF spectra of healthy subjects harboring different blood groups were acquired. Results showed the predominant occurrence of neutral and sialylated complex N-glycans with bisected N-acetylglucosamine and core- and/or antennary fucosylation. In the higher mass region, these species presented with multiple N-acetyllactosamine repeating units. Amongst the detected glycoforms, the presence of glycans bearing ABO(H) antigens allowed us to define a distinctive spectrum for each blood group. For the first time, advanced glycomic techniques have been applied to a comprehensive exploration of human RBC N-glycosylation, providing a new tool for the early detection of distinct glycome changes associated with disease conditions as well as for understanding the molecular recognition of pathogens.
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Wang B, Duan A, Xie S, Zhang J, Yuan L, Cao Q. The molecular imprinting of magnetic nanoparticles with boric acid affinity for the selective recognition and isolation of glycoproteins. RSC Adv 2021; 11:25524-25529. [PMID: 35478904 PMCID: PMC9036988 DOI: 10.1039/d1ra00716e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 07/18/2021] [Indexed: 11/21/2022] Open
Abstract
A strategy was designed for the molecular imprinting of magnetic nanoparticles with boric acid affinity (MNPs@MIP) which were then used for the selective recognition and isolation of glycoproteins. Fe3O4 nanoparticles were prepared by a solvothermal method and direct silanization by the condensation polymerization of aminopropyltriethoxysilane (APTES). Subsequently, phenylboric acid was functionalized by reductive amination between 2,3-difluoro-4-formyl phenylboric acid (DFFPBA) and the amido group. The resultant Fe3O4@SiO2–DFFPBA was then used for the selective adsorption of a glycoprotein template. Finally, a molecularly imprinted layer was covered on the surface nanoparticles by the condensation polymerization of tetraethyl orthosilicate (TEOS). The adsorption capacities of the resultant MNPs@MIP–HRP and MNPs@MIP–OVA to horseradish peroxidase (HRP) or ovalbumin (OVA) were significantly higher than non-imprinted particles (MNPs@NIP). Moreover, the adsorption capacities of MNPs@MIP–HRP and MNPs@MIP–OVA on non-template protein and non-glycoprotein bovine serum albumin (BSA) were significantly lower than those of their respective template proteins, thus indicating that both of the prepared MNPs@MIP exhibited excellent selectivity. A strategy was designed for the preparation of molecular imprinting of magnetic nanoparticles with boric acid affinity (MNPs@MIP), and the resultant MNPs@MIP exhibited excellent selectivity for template glycoproteins.![]()
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Affiliation(s)
- Bangjin Wang
- Department of Chemistry, Yunnan Normal University Kunming 650500 China
| | - Aihong Duan
- Department of Chemistry, Yunnan Normal University Kunming 650500 China
| | - Shengming Xie
- Department of Chemistry, Yunnan Normal University Kunming 650500 China
| | - Junhui Zhang
- Department of Chemistry, Yunnan Normal University Kunming 650500 China
| | - Liming Yuan
- Department of Chemistry, Yunnan Normal University Kunming 650500 China
| | - Qiue Cao
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education, School of Chemical Science and Technology, Yunnan University Kunming 650091 China
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24
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Abbasi DA, Nguyen TTA, Hall DA, Robertson-Dick E, Berry-Kravis E, Cologna SM. Characterization of the Cerebrospinal Fluid Proteome in Patients with Fragile X-Associated Tremor/Ataxia Syndrome. THE CEREBELLUM 2021; 21:86-98. [PMID: 34046842 DOI: 10.1007/s12311-021-01262-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 03/16/2021] [Indexed: 01/11/2023]
Abstract
Fragile X-associated tremor/ataxia syndrome (FXTAS), first described in 2001, is a neurodegenerative and movement disorder, caused by a premutation in the fragile X mental retardation 1 (FMR1) gene. To date, the biological mechanisms causing this condition are still not well understood, as not all premutation carriers develop FXTAS. To further understand this syndrome, we quantitatively compared the cerebrospinal fluid (CSF) proteome of FXTAS patients with age-matched controls using mass spectrometry. We identified 415 proteins of which 97 were altered in FXTAS patients. These proteins suggest changes in acute phase response signaling, liver X receptor/ retinoid X receptor (LXR/RXR) activation, and farnesoid X receptor (FXR)/RXR activation, which are the main pathways found to be affected. Additionally, we detected changes in many other proteins including amyloid-like protein 2, contactin-1, afamin, cell adhesion molecule 4, NPC intracellular cholesterol transporter 2, and cathepsin B, that had been previously noted to hold important roles in other movement disorders. Specific to RXR pathways, several apolipoproteins (APOA1, APOA2, APOA4, APOC2, and APOD) showed significant changes in the CSF of FXTAS patients. Lastly, CSF parameters were analyzed to investigate abnormalities in blood brain barrier function. Correlations were observed between patient albumin quotient values, a measure of permeability, and CGG repeat length as well as FXTAS rating scale scores.
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Affiliation(s)
- Diana A Abbasi
- Department of Pediatrics and Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
| | - Thu T A Nguyen
- Department of Chemistry, University of Illinois At Chicago, Chicago, IL, USA
| | - Deborah A Hall
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
| | - Erin Robertson-Dick
- Department of Communication Sciences and Disorders, Northwestern University, Chicago, IL, USA
| | - Elizabeth Berry-Kravis
- Department of Pediatrics and Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
| | - Stephanie M Cologna
- Department of Chemistry, University of Illinois At Chicago, Chicago, IL, USA.
- Laboratory of Integrated Neuroscience, University of Illinois At Chicago, 845 W Taylor Street, Room 4500, Chicago, IL, 60607, USA.
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25
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Tian Y, Tang R, Wang X, Zhou J, Li X, Ma S, Gong B, Ou J. Bioinspired dandelion-like silica nanoparticles modified with L-glutathione for highly efficient enrichment of N-glycopeptides in biological samples. Anal Chim Acta 2021; 1173:338694. [PMID: 34172155 DOI: 10.1016/j.aca.2021.338694] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 05/23/2021] [Indexed: 02/07/2023]
Abstract
The pretreatment of complicated biological samples to eliminate the interference of nonglycopeptides and improve the efficiency of glycopeptides detection is crucial in glycoproteomics research. Hydrophilic interaction chromatography (HILIC) has been adopted for enrichment of glycosylated peptides following identification with mass spectrometry, but it is still urgent to develop novel hydrophilic materials to save cost and improve enrichment efficiency. Scientists are pursuing to fabricate freestanding intelligent artificial materials. One promising approach is to use biomimic material. In our case, "one-pot" strategy was developed to prepare bioinspired nano-core-shell silica microspheres (CSSMs), employing tetrapropylorthosilicate as the silicon source and phenolic resin as the soft template. The pore structure of the obtained microspheres diverged from the center to the outside with diameter ranged from 150 to 340 nm, and shell layer ranged from 25 to 83 nm by adjusting the preparation parameters. Some of them showed dandelion-like morphology. After hydrophilic modification, these CSSMs exhibited great hydrophilicity and could be used as sorbents for enriching N-glycopeptides from complicated biological samples in HILIC. Up to 594 unique N-glycopeptides and 367 N-glycosylation sites from 182 N-glycoproteins were unambiguously identified from 2 μL of human serum, which was superior to the enrichment performance of many HILIC materials in reported papers, demonstrating great potential advantages in proteomic application.
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Affiliation(s)
- Yang Tian
- College of Chemistry and Chemical Engineering, North Minzu University, Yinchuan, 750021, China; CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Ruizhi Tang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Xia Wang
- College of Chemistry and Chemical Engineering, North Minzu University, Yinchuan, 750021, China; CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Jiahua Zhou
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaowei Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shujuan Ma
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.
| | - Bolin Gong
- College of Chemistry and Chemical Engineering, North Minzu University, Yinchuan, 750021, China.
| | - Junjie Ou
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China; University of Chinese Academy of Sciences, Beijing, 100049, China
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26
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High-throughput and high-sensitivity N-Glycan profiling: A platform for biopharmaceutical development and disease biomarker discovery. Anal Biochem 2021; 623:114205. [PMID: 33891963 DOI: 10.1016/j.ab.2021.114205] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 03/11/2021] [Accepted: 04/08/2021] [Indexed: 02/07/2023]
Abstract
Protein glycosylation contributes to critical biological function of glycoproteins. Glycan analysis is essential for the production of biopharmaceuticals as well as for the identification of disease biomarkers. However, glycans are highly heterogeneous, which has considerably hampered the progress of glycomics. Here, we present an improved 96-well plate format platform for streamlined glycan profiling that takes advantage of rapid glycoprotein denaturation, deglycosylation, fluorescent derivatization, and on-matrix glycan clean-up. This approach offers high sensitivity with consistent identification and quantification of diverse N-glycans across multiple samples on a high-throughput scale. We demonstrate its capability for N-glycan profiling of glycoproteins from various sources, including two recombinant monoclonal antibodies produced from Chinese Hamster Ovary cells, EG2-hFc and rituximab, polyclonal antibodies purified from human serum, and total glycoproteins from human serum. Combined with the complementary information obtained by sequential digestion from exoglycosidase arrays, this approach allows the detection and identification of multiple N-glycans in these complex biological samples. The reagents, workflow, and Hydrophilic interaction liquid chromatography with fluorescence detection (HILIC-FLD), are simple enough to be implemented into a straightforward user-friendly setup. This improved technology provides a powerful tool in support of rapid advancement of glycan analysis for biopharmaceutical development and biomarker discovery for clinical disease diagnosis.
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27
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Chen Z, Yu Q, Yu Q, Johnson J, Shipman R, Zhong X, Huang J, Asthana S, Carlsson C, Okonkwo O, Li L. In-depth Site-specific Analysis of N-glycoproteome in Human Cerebrospinal Fluid and Glycosylation Landscape Changes in Alzheimer's Disease. Mol Cell Proteomics 2021; 20:100081. [PMID: 33862227 PMCID: PMC8724636 DOI: 10.1016/j.mcpro.2021.100081] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 04/02/2021] [Accepted: 04/03/2021] [Indexed: 01/22/2023] Open
Abstract
As the body fluid that directly interchanges with the extracellular fluid of the central nervous system (CNS), cerebrospinal fluid (CSF) serves as a rich source for CNS-related disease biomarker discovery. Extensive proteome profiling has been conducted for CSF, but studies aimed at unraveling site-specific CSF N-glycoproteome are lacking. Initial efforts into site-specific N-glycoproteomics study in CSF yield limited coverage, hindering further experimental design of glycosylation-based disease biomarker discovery in CSF. In the present study, we have developed an N-glycoproteomic approach that combines enhanced N-glycopeptide sequential enrichment by hydrophilic interaction chromatography (HILIC) and boronic acid enrichment with electron transfer and higher-energy collision dissociation (EThcD) for large-scale intact N-glycopeptide analysis. The application of the developed approach to the analyses of human CSF samples enabled identifications of a total of 2893 intact N-glycopeptides from 511 N-glycosites and 285 N-glycoproteins. To our knowledge, this is the largest site-specific N-glycoproteome dataset reported for CSF to date. Such dataset provides molecular basis for a better understanding of the structure-function relationships of glycoproteins and their roles in CNS-related physiological and pathological processes. As accumulating evidence suggests that defects in glycosylation are involved in Alzheimer's disease (AD) pathogenesis, in the present study, a comparative in-depth N-glycoproteomic analysis was conducted for CSF samples from healthy control and AD patients, which yielded a comparable N-glycoproteome coverage but a distinct expression pattern for different categories of glycoforms, such as decreased fucosylation in AD CSF samples. Altered glycosylation patterns were detected for a number of N-glycoproteins including alpha-1-antichymotrypsin, ephrin-A3 and carnosinase CN1 etc., which serve as potentially interesting targets for further glycosylation-based AD study and may eventually lead to molecular elucidation of the role of glycosylation in AD progression.
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Affiliation(s)
- Zhengwei Chen
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin, USA
| | - Qinying Yu
- School of Pharmacy, University of Wisconsin, Madison, Wisconsin, USA
| | - Qing Yu
- School of Pharmacy, University of Wisconsin, Madison, Wisconsin, USA
| | - Jillian Johnson
- School of Pharmacy, University of Wisconsin, Madison, Wisconsin, USA
| | - Richard Shipman
- Department of Applied Science, University of Wisconsin-Stout, Menomonie, Wisconsin, USA
| | - Xiaofang Zhong
- School of Pharmacy, University of Wisconsin, Madison, Wisconsin, USA
| | - Junfeng Huang
- School of Pharmacy, University of Wisconsin, Madison, Wisconsin, USA
| | - Sanjay Asthana
- School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin, USA
| | - Cynthia Carlsson
- School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin, USA
| | - Ozioma Okonkwo
- School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin, USA
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin, USA; School of Pharmacy, University of Wisconsin, Madison, Wisconsin, USA.
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28
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Ye L, Fang YS, Li XX, Gao Y, Liu SS, Chen Q, Wu Q, Cheng HW, Du WD. A simple lectin-based biochip might display the potential clinical value of glycomics in patients with spontaneous intracerebral hemorrhage. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:544. [PMID: 33987242 DOI: 10.21037/atm-20-7315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Background Intracerebral hemorrhage (ICH) is a cerebrovascular disease with extremely high disability and mortality rates. Glycans play critical roles in biological processes. However, whether glycans can serve as potential biomarkers for determining clinical diagnosis and prognosis in ICH remains determined. Methods In this study, we established a lectin-biochip to measure serum glycans levels in ICH patients (n=48) and healthy controls (n=16). An enzyme-linked immunosorbent assay (ELISA) was carried out to determine serum levels of IL-10 and TNF-α in the patients. Correlation analyses of the serum glycan and cytokine levels and the clinicopathological parameters of patients were performed. Results The biochip-based data revealed that the serum levels of α-Man/α-Glc (ConA), Galβ3GalNAc (PNA), GalNAc (VVA), Fucα6GlcNAc (AAL), α-Fuc (LTL), and Galβ3GalNAc-Ser/Thr (AIL) significantly increased in the super-acute phase of ICH in comparison with healthy controls. Clinicopathological analysis indicated the serum levels of ConA, VVA, and LTL had significant associations with the National Institute of Health Stroke Scale (NIHSS), and serum VVA levels had a significant association with the Mini-Mental State Examination (MMSE) at day 90 after ICH. Correlation coefficient analysis revealed significant correlations between TNF-α and ConA (P<0.001) as well as between IL-10 and ConA (P<0.001), PNA (P=0.02), VVA (P<0.001), and MAL (P=0.04), respectively. Conclusions We established a proof-of-concept platform for detecting serum glycomics and highlighted their potential value in diagnosing and predicting ICH patients' outcomes.
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Affiliation(s)
- Lei Ye
- Department of Neurosurgery, the First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Yong-Sheng Fang
- Department of Pathology, the Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Xiao-Xue Li
- Institute of Pathology, University Medical Center Göttingen, Göttingen, Germany
| | - Yi Gao
- Department of Pathology, Anhui Medical University, Hefei, China
| | - Sheng-Sheng Liu
- Department of Pathology, Anhui Medical University, Hefei, China
| | - Qiang Chen
- Department of Pathology, Anhui Medical University, Hefei, China
| | - Qiang Wu
- Department of Pathology, the Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Hong-Wei Cheng
- Department of Neurosurgery, the First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Wei-Dong Du
- Department of Pathology, Anhui Medical University, Hefei, China
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29
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Silbern I, Fang P, Ji Y, Christof L, Urlaub H, Pan KT. Relative Quantification of Phosphorylated and Glycosylated Peptides from the Same Sample Using Isobaric Chemical Labelling with a Two-Step Enrichment Strategy. Methods Mol Biol 2021; 2228:185-203. [PMID: 33950492 DOI: 10.1007/978-1-0716-1024-4_14] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Post-translational modifications (PTMs) are essential for the regulation of all cellular processes. The interplay of various PTMs on a single protein or different proteins comprises a complexity that we are far from understanding in its entirety. Reliable strategies for the enrichment and accurate quantification of PTMs are needed to study as many PTMs on proteins as possible. In this protocol we present a liquid chromatography-tandem mass spectrometry (LC/MS/MS)-based workflow that enables the enrichment and quantification of phosphorylated and N-glycosylated peptides from the same sample. After extraction and digestion of proteins, we label the peptides with stable isotope-coded tandem mass tags (TMTs) and enrich N-glycopeptides and phosphopeptides by using zwitterionic hydrophilic interaction chromatography (ZIC-HILIC) and titanium dioxide (TiO2) beads, respectively. Labelled and enriched N-glycopeptides and phosphopeptides are further separated by high pH (basic) reversed-phase chromatography and analyzed by LC/MS/MS. The enrichment strategies, together with quantification of two different PTM types from the same sample, allow investigation of the interplay of those two PTMs, which are important for signal transduction inside the cell (phosphorylation), as well as for messaging between cells through decoration of the cellular surface (glycosylation).
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Affiliation(s)
- Ivan Silbern
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Goettingen, Germany
- Bioanalytics Group, Institute of Clinical Chemistry, University Medical Center Goettingen, Goettingen, Germany
| | - Pan Fang
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Goettingen, Germany
| | - Yanlong Ji
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Goettingen, Germany
- Hematology/Oncology, Department of Medicine II, Johann Wolfgang Goethe University, Frankfurt, Germany
- Frankfurt Cancer Institute, Goethe University, Frankfurt am Main, Germany
| | - Lenz Christof
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Goettingen, Germany
- Bioanalytics Group, Institute of Clinical Chemistry, University Medical Center Goettingen, Goettingen, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Goettingen, Germany.
- Bioanalytics Group, Institute of Clinical Chemistry, University Medical Center Goettingen, Goettingen, Germany.
- Hematology/Oncology, Department of Medicine II, Johann Wolfgang Goethe University, Frankfurt, Germany.
| | - Kuan-Ting Pan
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Goettingen, Germany.
- Hematology/Oncology, Department of Medicine II, Johann Wolfgang Goethe University, Frankfurt, Germany.
- Frankfurt Cancer Institute, Goethe University, Frankfurt am Main, Germany.
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30
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Abstract
Glycobiology is a glycan-based field of study that focuses on the structure, function, and biology of carbohydrates, and glycomics is a sub-study of the field of glycobiology that aims to define structure/function of glycans in living organisms. With the popularity of the glycobiology and glycomics, application of computational modeling expanded in the scientific area of glycobiology over the last decades. The recent availability of progressive Wet-Lab methods in the field of glycobiology and glycomics is promising for the impact of systems biology on the research area of the glycome, an emerging field that is termed “systems glycobiology.” This chapter will summarize the up-to-date leading edge in the use of bioinformatics tools in the field of glycobiology. The chapter provides basic knowledge both for glycobiologists interested in the application of bioinformatics tools and scientists of computational biology interested in studying the glycome.
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31
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Tiwari D, Jakhmola S, Pathak DK, Kumar R, Jha HC. Temporal In Vitro Raman Spectroscopy for Monitoring Replication Kinetics of Epstein-Barr Virus Infection in Glial Cells. ACS OMEGA 2020; 5:29547-29560. [PMID: 33225186 PMCID: PMC7676301 DOI: 10.1021/acsomega.0c04525] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 10/21/2020] [Indexed: 05/17/2023]
Abstract
Raman spectroscopy can be used as a tool to study virus entry and pathogen-driven manipulation of the host efficiently. To date, Epstein-Barr virus (EBV) entry and altered biochemistry of the glial cell upon infection are elusive. In this study, we detected biomolecular changes in human glial cells, namely, HMC-3 (microglia) and U-87 MG (astrocytes), at two variable cellular locations (nucleus and periphery) by Raman spectroscopy post-EBV infection at different time points. Two possible phenomena, one attributed to the response of the cell to viral attachment and invasion and the other involved in duplication of the virus followed by egress from the host cell, are investigated. These changes corresponded to unique Raman spectra associated with specific biomolecules in the infected and the uninfected cells. The Raman signals from the nucleus and periphery of the cell also varied, indicating differential biochemistry and signaling processes involved in infection progression at these locations. Molecules such as cholesterol, glucose, hyaluronan, phenylalanine, phosphoinositide, etc. are associated with the alterations in the cellular biochemical homeostasis. These molecules are mainly responsible for cellular processes such as lipid transport, cell proliferation, differentiation, and apoptosis in the cells. Raman signatures of these molecules at distinct time points of infection indicated their periodic involvement, depending on the stage of virus infection. Therefore, it is possible to discern the details of variability in EBV infection progression in glial cells at the biomolecular level using time-dependent in vitro Raman scattering.
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Affiliation(s)
- Deeksha Tiwari
- Discipline
of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, 453552 Indore, India
| | - Shweta Jakhmola
- Discipline
of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, 453552 Indore, India
| | - Devesh K. Pathak
- Discipline
of Physics, Indian Institute of Technology
Indore, Simrol, 453552 Indore, India
| | - Rajesh Kumar
- Discipline
of Physics, Indian Institute of Technology
Indore, Simrol, 453552 Indore, India
- Centre
for Advanced Electronics, Indian Institute
of Technology Indore, Simrol, 453552 Indore, India
| | - Hem Chandra Jha
- Discipline
of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, 453552 Indore, India
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32
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Lee JA, Hall B, Allsop J, Alqarni R, Allen SP. Lipid metabolism in astrocytic structure and function. Semin Cell Dev Biol 2020; 112:123-136. [PMID: 32773177 DOI: 10.1016/j.semcdb.2020.07.017] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 06/18/2020] [Accepted: 07/29/2020] [Indexed: 02/06/2023]
Abstract
Astrocytes are the most abundant glial cell in the central nervous system and are involved in multiple processes including metabolic homeostasis, blood brain barrier regulation and neuronal crosstalk. Astrocytes are the main storage point of glycogen in the brain and it is well established that astrocyte uptake of glutamate and release of lactate prevents neuronal excitability and supports neuronal metabolic function. However, the role of lipid metabolism in astrocytes in relation to neuronal support has been until recently, unclear. Lipids play a fundamental role in astrocyte function, including energy generation, membrane fluidity and cell to cell signaling. There is now emerging evidence that astrocyte storage of lipids in droplets has a crucial physiological and protective role in the central nervous system. This pathway links β-oxidation in astrocytes to inflammation, signalling, oxidative stress and mitochondrial energy generation in neurons. Disruption in lipid metabolism, structure and signalling in astrocytes can lead to pathogenic mechanisms associated with a range of neurological disorders.
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Affiliation(s)
- James Ak Lee
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK
| | - Benjamin Hall
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK
| | - Jessica Allsop
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK
| | - Razan Alqarni
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK
| | - Scott P Allen
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK.
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Ukaegbu OI, DeMeester KE, Liang H, Brown AR, Jones ZS, Grimes CL. Utility of bacterial peptidoglycan recycling enzymes in the chemoenzymatic synthesis of valuable UDP sugar substrates. Methods Enzymol 2020; 638:1-26. [PMID: 32416908 DOI: 10.1016/bs.mie.2020.02.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Uridine diphosphate (UDP) sugars are essential precursors for glycosylation reactions in all forms of life. Reactions that transfer the carbohydrate from the UDP donor are catalyzed by glycosyltransferases (Gtfs). While the stereochemistry and negative physiological charge of UDP-sugars are essential for their biochemical function in the cell, these characteristics make them challenging molecules to synthesize and purify on scale in the laboratory. This chapter focuses on the utilization of a chemoenzymatic synthesis of muramyl UDP-sugars, key building blocks in the bacterial cell peptidoglycan. A scalable strategy to obtain UDP-N-acetyl muramic acid derivatives (UDP-NAM), the first committed intermediate used solely in peptidoglycan biosynthesis, is described herein. This methodology utilizes two enzymes involving the cell wall recycling enzymes MurNAc/GlcNAc anomeric kinase (AmgK) and NAM α-1-phosphate uridylyl transferase (MurU), respectively. The promiscuity of these enzymes allows for the unique chemical functionality to be embedded in bacterial peptidoglycan both in vitro and in whole bacterial cells for subsequent structural and functional studies of this important biopolymer.
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Affiliation(s)
- Ophelia I Ukaegbu
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, United States
| | - Kristen E DeMeester
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, United States
| | - Hai Liang
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, United States
| | - Ashley R Brown
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, United States
| | - Zachary S Jones
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, United States
| | - Catherine Leimkuhler Grimes
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, United States; Department of Biological Sciences, University of Delaware, Newark, DE, United States.
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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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Tommasone S, Allabush F, Tagger YK, Norman J, Köpf M, Tucker JHR, Mendes PM. The challenges of glycan recognition with natural and artificial receptors. Chem Soc Rev 2019; 48:5488-5505. [PMID: 31552920 DOI: 10.1039/c8cs00768c] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Glycans - simple or complex carbohydrates - play key roles as recognition determinants and modulators of numerous physiological and pathological processes. Thus, many biotechnological, diagnostic and therapeutic opportunities abound for molecular recognition entities that can bind glycans with high selectivity and affinity. This review begins with an overview of the current biologically and synthetically derived glycan-binding scaffolds that include antibodies, lectins, aptamers and boronic acid-based entities. It is followed by a more detailed discussion on various aspects of their generation, structure and recognition properties. It serves as the basis for highlighting recent key developments and technical challenges that must be overcome in order to fully deal with the specific recognition of a highly diverse and complex range of glycan structures.
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Affiliation(s)
- Stefano Tommasone
- School of Chemical Engineering, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
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36
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Kelley AR, Bach SB, Perry G. Analysis of post-translational modifications in Alzheimer's disease by mass spectrometry. Biochim Biophys Acta Mol Basis Dis 2019; 1865:2040-2047. [DOI: 10.1016/j.bbadis.2018.11.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 10/19/2018] [Accepted: 11/04/2018] [Indexed: 01/09/2023]
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Xiao H, Sun F, Suttapitugsakul S, Wu R. Global and site-specific analysis of protein glycosylation in complex biological systems with Mass Spectrometry. MASS SPECTROMETRY REVIEWS 2019; 38:356-379. [PMID: 30605224 PMCID: PMC6610820 DOI: 10.1002/mas.21586] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Accepted: 11/27/2018] [Indexed: 05/16/2023]
Abstract
Protein glycosylation is ubiquitous in biological systems and plays essential roles in many cellular events. Global and site-specific analysis of glycoproteins in complex biological samples can advance our understanding of glycoprotein functions and cellular activities. However, it is extraordinarily challenging because of the low abundance of many glycoproteins and the heterogeneity of glycan structures. The emergence of mass spectrometry (MS)-based proteomics has provided us an excellent opportunity to comprehensively study proteins and their modifications, including glycosylation. In this review, we first summarize major methods for glycopeptide/glycoprotein enrichment, followed by the chemical and enzymatic methods to generate a mass tag for glycosylation site identification. We next discuss the systematic and quantitative analysis of glycoprotein dynamics. Reversible protein glycosylation is dynamic, and systematic study of glycoprotein dynamics helps us gain insight into glycoprotein functions. The last part of this review focuses on the applications of MS-based proteomics to study glycoproteins in different biological systems, including yeasts, plants, mice, human cells, and clinical samples. Intact glycopeptide analysis is also included in this section. Because of the importance of glycoproteins in complex biological systems, the field of glycoproteomics will continue to grow in the next decade. Innovative and effective MS-based methods will exponentially advance glycoscience, and enable us to identify glycoproteins as effective biomarkers for disease detection and drug targets for disease treatment. © 2019 Wiley Periodicals, Inc. Mass Spec Rev 9999: XX-XX, 2019.
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Affiliation(s)
- Haopeng Xiao
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta 30332 Georgia
| | - Fangxu Sun
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta 30332 Georgia
| | - Suttipong Suttapitugsakul
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta 30332 Georgia
| | - Ronghu Wu
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta 30332 Georgia
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Matsuda-Lennikov M, Biancalana M, Zou J, Ravell JC, Zheng L, Kanellopoulou C, Jiang P, Notarangelo G, Jing H, Masutani E, Oler AJ, Olano LR, Schulz BL, Lenardo MJ. Magnesium transporter 1 (MAGT1) deficiency causes selective defects in N-linked glycosylation and expression of immune-response genes. J Biol Chem 2019; 294:13638-13656. [PMID: 31337704 DOI: 10.1074/jbc.ra119.008903] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 07/08/2019] [Indexed: 12/22/2022] Open
Abstract
Magnesium transporter 1 (MAGT1) critically mediates magnesium homeostasis in eukaryotes and is highly-conserved across different evolutionary branches. In humans, loss-of-function mutations in the MAGT1 gene cause X-linked magnesium deficiency with Epstein-Barr virus (EBV) infection and neoplasia (XMEN), a disease that has a broad range of clinical and immunological consequences. We have previously shown that EBV susceptibility in XMEN is associated with defective expression of the antiviral natural-killer group 2 member D (NKG2D) protein and abnormal Mg2+ transport. New evidence suggests that MAGT1 is the human homolog of the yeast OST3/OST6 proteins that form an integral part of the N-linked glycosylation complex, although the exact contributions of these perturbations in the glycosylation pathway to disease pathogenesis are still unknown. Using MS-based glycoproteomics, along with CRISPR/Cas9-KO cell lines, natural killer cell-killing assays, and RNA-Seq experiments, we now demonstrate that humans lacking functional MAGT1 have a selective deficiency in both immune and nonimmune glycoproteins, and we identified several critical glycosylation defects in important immune-response proteins and in the expression of genes involved in immunity, particularly CD28. We show that MAGT1 function is partly interchangeable with that of the paralog protein tumor-suppressor candidate 3 (TUSC3) but that each protein has a different tissue distribution in humans. We observed that MAGT1-dependent glycosylation is sensitive to Mg2+ levels and that reduced Mg2+ impairs immune-cell function via the loss of specific glycoproteins. Our findings reveal that defects in protein glycosylation and gene expression underlie immune defects in an inherited disease due to MAGT1 deficiency.
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Affiliation(s)
- Mami Matsuda-Lennikov
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, NIAID, National Institutes of Health, Bethesda, Maryland 20892.,Clinical Genomics Program, NIAID, National Institutes of Health, Bethesda, Maryland 20892
| | - Matthew Biancalana
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, NIAID, National Institutes of Health, Bethesda, Maryland 20892.,Clinical Genomics Program, NIAID, National Institutes of Health, Bethesda, Maryland 20892
| | - Juan Zou
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, NIAID, National Institutes of Health, Bethesda, Maryland 20892.,Clinical Genomics Program, NIAID, National Institutes of Health, Bethesda, Maryland 20892
| | - Juan C Ravell
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, NIAID, National Institutes of Health, Bethesda, Maryland 20892.,Clinical Genomics Program, NIAID, National Institutes of Health, Bethesda, Maryland 20892
| | - Lixin Zheng
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, NIAID, National Institutes of Health, Bethesda, Maryland 20892.,Clinical Genomics Program, NIAID, National Institutes of Health, Bethesda, Maryland 20892
| | - Chrysi Kanellopoulou
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, NIAID, National Institutes of Health, Bethesda, Maryland 20892.,Clinical Genomics Program, NIAID, National Institutes of Health, Bethesda, Maryland 20892
| | - Ping Jiang
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, NIAID, National Institutes of Health, Bethesda, Maryland 20892.,Clinical Genomics Program, NIAID, National Institutes of Health, Bethesda, Maryland 20892
| | - Giulia Notarangelo
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, NIAID, National Institutes of Health, Bethesda, Maryland 20892.,Clinical Genomics Program, NIAID, National Institutes of Health, Bethesda, Maryland 20892
| | - Huie Jing
- Clinical Genomics Program, NIAID, National Institutes of Health, Bethesda, Maryland 20892.,Human Immunological Diseases Section, Laboratory of Clinical Immunology and Microbiology, NIAID, National Institutes of Health, Bethesda, Maryland 20892
| | - Evan Masutani
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, NIAID, National Institutes of Health, Bethesda, Maryland 20892.,Clinical Genomics Program, NIAID, National Institutes of Health, Bethesda, Maryland 20892
| | - Andrew J Oler
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, NIAID, National Institutes of Health, Bethesda, Maryland 20892
| | - Lisa Renee Olano
- Laboratory of Neurotoxicology, National Institute of Mental Health, Bethesda, Maryland 20892
| | - Benjamin L Schulz
- University of Queensland, School of Chemistry and Molecular Biology, Brisbane, St. Lucia, Queensland 4072, Australia
| | - Michael J Lenardo
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, NIAID, National Institutes of Health, Bethesda, Maryland 20892 .,Clinical Genomics Program, NIAID, National Institutes of Health, Bethesda, Maryland 20892
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Mitchell P, Tommasone S, Angioletti-Uberti S, Bowen J, Mendes PM. Precise Generation of Selective Surface-Confined Glycoprotein Recognition Sites. ACS APPLIED BIO MATERIALS 2019; 2:2617-2623. [PMID: 31259319 PMCID: PMC6591769 DOI: 10.1021/acsabm.9b00289] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 05/12/2019] [Indexed: 12/31/2022]
Abstract
![]()
Since
glycoproteins have become increasingly recognized as key
players in a wide variety of disease processes, there is an increasing
need for advanced affinity materials for highly selective glycoprotein
binding. Herein, for the first time, a surface-initiated controlled
radical polymerization is integrated with supramolecular templating
and molecular imprinting to yield highly reproducible synthetic recognition
sites on surfaces with dissociation constants (KD) in the low micromolar range for target glycoproteins and
minimal binding to nontarget glycoproteins. Importantly, it is shown
that the synthetic strategy has a remarkable ability to distinguish
the glycosylated and nonglycosylated forms of the same glycoprotein,
with a >5-fold difference in binding affinity. The precise control
over the polymer film thickness and positioning of multiple carbohydrate
receptors plays a crucial role in achieving an enhanced affinity and
selectivity. The generated functional materials of unprecedented glycoprotein
recognition performance open up a wealth of opportunities in the biotechnological
and biomedical fields.
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Affiliation(s)
- Philippa Mitchell
- School of Chemical Engineering, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Stefano Tommasone
- School of Chemical Engineering, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Stefano Angioletti-Uberti
- Faculty of Engineering, Department of Materials, Imperial College London, London SW7 2AZ, United Kingdom
| | - James Bowen
- Faculty of Science, Technology, Engineering & Mathematics, The Open University, Milton Keynes MK7 6AA, United Kingdom
| | - Paula M Mendes
- School of Chemical Engineering, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
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40
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Glycoproteomics and Glycomics in the Biomedical Area Special Issue. Proteomics Clin Appl 2019; 12:e1800122. [PMID: 30203442 DOI: 10.1002/prca.201800122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Indexed: 11/10/2022]
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Redenšek S, Flisar D, Kojović M, Kramberger MG, Georgiev D, Pirtošek Z, Trošt M, Dolžan V. Genetic variability of inflammation and oxidative stress genes does not play a major role in the occurrence of adverse events of dopaminergic treatment in Parkinson's disease. J Neuroinflammation 2019; 16:50. [PMID: 30813952 PMCID: PMC6393982 DOI: 10.1186/s12974-019-1439-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 02/18/2019] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Inflammation and oxidative stress are recognized as important contributors to Parkinson's disease pathogenesis. As such, genetic variability in these pathways could have a role in susceptibility for the disease as well as in the treatment outcome. Dopaminergic treatment is effective in management of motor symptoms, but poses a risk for motor and non-motor adverse events. Our aim was to evaluate the impact of selected single-nucleotide polymorphisms in genes involved in inflammation and oxidative stress on Parkinson's disease susceptibility and the occurrence of adverse events of dopaminergic treatment. METHODS In total, 224 patients were enrolled, and their demographic and clinical data on the disease course were collected. Furthermore, a control group of 146 healthy Slovenian blood donors were included for Parkinson's disease' risk evaluation. Peripheral blood was obtained for DNA isolation. Genotyping was performed for NLRP3 rs35829419, CARD8 rs2043211, IL1β rs16944, IL1β rs1143623, IL6 rs1800795, CAT rs1001179, CAT rs10836235, SOD2 rs4880, NOS1 rs2293054, NOS1 rs2682826, TNF-α rs1800629, and GPX1 rs1050450. Logistic regression was used for analysis of possible associations. RESULTS We observed a nominally significant association of the IL1β rs1143623 C allele with the risk for Parkinson's disease (OR = 0.59; 95%CI = 0.38-0.92, p = 0.021). CAT rs1001179 A allele was significantly associated with peripheral edema (OR = 0.32; 95%CI = 0.15-0.68; p = 0.003). Other associations observed were only nominally significant after adjustments: NOS1 rs2682826 A allele and excessive daytime sleepiness and sleep attacks (OR = 1.75; 95%CI = 1.00-3.06, p = 0.048), SOD2 rs4880 T allele and nausea/vomiting (OR = 0.49, 95%CI = 0.25-0.94; p = 0.031), IL1β rs1143623 C allele and orthostatic hypotension (OR = 0.57, 95%CI = 0.32-1.00, p = 0.050), and NOS1 rs2682826 A allele and impulse control disorders (OR = 2.59; 95%CI = 1.09-6.19; p = 0.032). We did not find any associations between selected polymorphisms and motor adverse events. CONCLUSIONS Apart from some nominally significant associations, one significant association between CAT genetic variability and peripheral edema was observed as well. Therefore, the results of our study suggest some links between genetic variability in inflammation- and oxidative stress-related pathways and non-motor adverse events of dopaminergic treatment. However, the investigated polymorphisms do not play a major role in the occurrence of the disease and the adverse events of dopaminergic treatment.
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Affiliation(s)
- Sara Redenšek
- Pharmacogenetics Laboratory, Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Vrazov trg 2, 1000 Ljubljana, Slovenia
| | - Dušan Flisar
- Department of Neurology, University Medical Centre Ljubljana, Zaloška cesta 2, 1000 Ljubljana, Slovenia
| | - Maja Kojović
- Department of Neurology, University Medical Centre Ljubljana, Zaloška cesta 2, 1000 Ljubljana, Slovenia
| | | | - Dejan Georgiev
- Department of Neurology, University Medical Centre Ljubljana, Zaloška cesta 2, 1000 Ljubljana, Slovenia
| | - Zvezdan Pirtošek
- Department of Neurology, University Medical Centre Ljubljana, Zaloška cesta 2, 1000 Ljubljana, Slovenia
| | - Maja Trošt
- Department of Neurology, University Medical Centre Ljubljana, Zaloška cesta 2, 1000 Ljubljana, Slovenia
| | - Vita Dolžan
- Pharmacogenetics Laboratory, Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Vrazov trg 2, 1000 Ljubljana, Slovenia
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Cilento EM, Jin L, Stewart T, Shi M, Sheng L, Zhang J. Mass spectrometry: A platform for biomarker discovery and validation for Alzheimer's and Parkinson's diseases. J Neurochem 2019; 151:397-416. [PMID: 30474862 DOI: 10.1111/jnc.14635] [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: 10/01/2018] [Revised: 11/15/2018] [Accepted: 11/19/2018] [Indexed: 12/16/2022]
Abstract
Accurate, reliable, and objective biomarkers for Alzheimer's disease (AD), Parkinson's disease (PD), and related age-associated neurodegenerative disorders are urgently needed to assist in both diagnosis, particularly at early stages, and monitoring of disease progression. Technological advancements in protein detection platforms over the last few decades have resulted in a plethora of reported molecular biomarker candidates for both AD and PD; however, very few of these candidates are developed beyond the discovery phase of the biomarker development pipeline, a reflection of the current bottleneck within the field. In this review, the expanded use of selected reaction monitoring (SRM) targeted mass spectrometry will be discussed in detail as a platform for systematic verification of large panels of protein biomarker candidates prior to costly validation testing. We also advocate for the coupling of discovery-based proteomics with modern targeted MS-based approaches (e.g., SRM) within a single study in future workflows to expedite biomarker development and validation for AD and PD. It is our hope that improving the efficiency within the biomarker development process by use of an SRM pipeline may ultimately hasten the development of biomarkers that both decrease misdiagnosis of AD and PD and ultimately lead to detection at early stages of disease and objective assessment of disease progression. This article is part of the special issue "Proteomics".
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Affiliation(s)
- Eugene M Cilento
- Department of Pathology, University of Washington, School of Medicine, Seattle, Washington, USA
| | - Lorrain Jin
- Department of Pathology, University of Washington, School of Medicine, Seattle, Washington, USA
| | - Tessandra Stewart
- Department of Pathology, University of Washington, School of Medicine, Seattle, Washington, USA
| | - Min Shi
- Department of Pathology, University of Washington, School of Medicine, Seattle, Washington, USA
| | - Lifu Sheng
- Department of Pathology, University of Washington, School of Medicine, Seattle, Washington, USA
| | - Jing Zhang
- Department of Pathology, University of Washington, School of Medicine, Seattle, Washington, USA.,Department of Pathology, School of Basic Medicine, Peking University Health Science Center, Peking University Third Hospital and Peking Key Laboratory for Early Diagnosis of Neurodegenerative Disorders, Beijing, China
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Patel S, Sangeeta S. Pesticides as the drivers of neuropsychotic diseases, cancers, and teratogenicity among agro-workers as well as general public. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2019; 26:91-100. [PMID: 30411285 DOI: 10.1007/s11356-018-3642-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 10/30/2018] [Indexed: 06/08/2023]
Abstract
The need to maximize agricultural productivity has made pesticides an indispensable part of current times. Farmers are unaware of the lurking consequences of the pesticide exposure, which endanger their health. It also puts the unsuspecting consumers in peril. The pesticides (from organophosphates, organochlorine, and carbamate class) disrupt the immune and hormonal signaling, causing recurrent inflammation, which leads to a wide array pathologies, including teratogenicity. Numerous farmers have fallen victim to neural disorders-driven suicides and lungs, prostate/breast cancer-caused untimely deaths. Green revolution which significantly escalated agricultural productivity is backfiring now. It is high time that environmental and agricultural authorities act to restrain the excessive usage of the detrimental chemicals and educate farmers regarding the crisis. This review discusses the biological mechanisms of pesticide-driven pathogenesis (such as the activation or inhibition of caspase, serine protease, acetylcholinesterase) and presents the pesticide-exposure-caused health deterioration in USA, India, and Africa. This holistic and critical review should be an eye-opener for general public, and a guide for researchers.
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Affiliation(s)
- Seema Patel
- Bioinformatics and Medical Informatics Research Center, San Diego State University, 5500 Campanile Dr, San Diego, CA, 92182, USA.
| | - Sushree Sangeeta
- Department of Ecology and Environmental Sciences, Pondicherry University, Puducherry, 605014, India.
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44
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Understanding cellular glycan surfaces in the central nervous system. Biochem Soc Trans 2018; 47:89-100. [PMID: 30559272 DOI: 10.1042/bst20180330] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 10/21/2018] [Accepted: 11/06/2018] [Indexed: 02/06/2023]
Abstract
Glycosylation, the enzymatic process by which glycans are attached to proteins and lipids, is the most abundant and functionally important type of post-translational modification associated with brain development, neurodegenerative disorders, psychopathologies and brain cancers. Glycan structures are diverse and complex; however, they have been detected and targeted in the central nervous system (CNS) by various immunohistochemical detection methods using glycan-binding proteins such as anti-glycan antibodies or lectins and/or characterized with analytical techniques such as chromatography and mass spectrometry. The glycan structures on glycoproteins and glycolipids expressed in neural stem cells play key roles in neural development, biological processes and CNS maintenance, such as cell adhesion, signal transduction, molecular trafficking and differentiation. This brief review will highlight some of the important findings on differential glycan expression across stages of CNS cell differentiation and in pathological disorders and diseases such as Alzheimer's disease, Parkinson's disease, Huntington's disease, multiple sclerosis, amyotrophic lateral sclerosis, schizophrenia and brain cancer.
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45
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Chen Z, Yu Q, Hao L, Liu F, Johnson J, Tian Z, Kao WJ, Xu W, Li L. Site-specific characterization and quantitation of N-glycopeptides in PKM2 knockout breast cancer cells using DiLeu isobaric tags enabled by electron-transfer/higher-energy collision dissociation (EThcD). Analyst 2018; 143:2508-2519. [PMID: 29687791 PMCID: PMC5975206 DOI: 10.1039/c8an00216a] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The system-wide site-specific analysis of intact glycopeptides is crucial for understanding the exact functional relevance of protein glycosylation. A dedicated workflow with the capability to simultaneously characterize and quantify intact glycopeptides in a site-specific and high-throughput manner is essential to reveal specific glycosylation alteration patterns in complex biological systems. In this study, an enhanced, dedicated, large-scale site-specific quantitative N-glycoproteomics workflow has been established, which includes improved specific extraction of membrane-bound glycoproteins using the filter aided sample preparation (FASP) method, enhanced enrichment of N-glycopeptides using sequential hydrophilic interaction liquid chromatography (HILIC) and multi-lectin affinity (MLA) enrichment, site-specific N-glycopeptide characterization enabled by EThcD, relative quantitation utilizing isobaric N,N-dimethyl leucine (DiLeu) tags and automated FDR-based large-scale data analysis by Byonic. For the first time, our study shows that HILIC complements to a very large extent to MLA enrichment with only 20% overlapping in enriching intact N-glycopeptides. When applying the developed workflow to site-specific N-glycoproteome study in PANC1 cells, we were able to identify 1067 intact N-glycopeptides, representing 311 glycosylation sites and 88 glycan compositions from 205 glycoproteins. We further applied this approach to study the glycosylation alterations in PKM2 knockout cells vs. parental breast cancer cells and revealed altered N-glycoprotein/N-glycopeptide patterns and very different glycosylation microheterogeneity for different types of glycans. To obtain a more comprehensive map of glycoprotein alterations, N-glycopeptides after treatment with PNGase F were also analyzed. A total of 484 deglycosylated peptides were quantified, among which 81 deglycosylated peptides from 70 glycoproteins showed significant changes. KEGG pathway analysis revealed that the PI3K/Akt signaling pathway was highly enriched, which provided evidence to support the previous finding that PKM2 knockdown cancer cells rely on activation of Akt for their survival. With glycosylation being one of the most important signaling modulators, our results provide additional evidence that signaling pathways are closely regulated by metabolism.
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Affiliation(s)
- Zhengwei Chen
- Department of Chemistry, University of Wisconsin, Madison, WI 53705, USA
| | - Qing Yu
- School of Pharmacy, University of Wisconsin, Madison, WI 53705, USA
| | - Ling Hao
- School of Pharmacy, University of Wisconsin, Madison, WI 53705, USA
| | - Fabao Liu
- McArdle Laboratory for Cancer Research, University of Wisconsin, Madison, WI 53705, USA
| | - Jillian Johnson
- School of Pharmacy, University of Wisconsin, Madison, WI 53705, USA
| | - Zichuan Tian
- Department of Chemistry, University of Wisconsin, Madison, WI 53705, USA
| | - W. John Kao
- School of Pharmacy, University of Wisconsin, Madison, WI 53705, USA
| | - Wei Xu
- McArdle Laboratory for Cancer Research, University of Wisconsin, Madison, WI 53705, USA
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin, Madison, WI 53705, USA
- School of Pharmacy, University of Wisconsin, Madison, WI 53705, USA
- School of Life Sciences, Tianjin University, Tianjin, 300072, P.R. China
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46
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Frost DC, Li L. Recent advances in mass spectrometry-based glycoproteomics. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2018; 95:71-123. [PMID: 24985770 DOI: 10.1016/b978-0-12-800453-1.00003-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Protein glycosylation plays fundamental roles in many biological processes as one of the most common, and the most complex, posttranslational modification. Alterations in glycosylation profile are now known to be associated with many diseases. As a result, the discovery and detailed characterization of glycoprotein disease biomarkers is a primary interest of biomedical research. Advances in mass spectrometry (MS)-based glycoproteomics and glycomics are increasingly enabling qualitative and quantitative approaches for site-specific structural analysis of protein glycosylation. While the complexity presented by glycan heterogeneity and the wide dynamic range of clinically relevant samples like plasma, serum, cerebrospinal fluid, and tissue make comprehensive analyses of the glycoproteome a challenging task, the ongoing efforts into the development of glycoprotein enrichment, enzymatic digestion, and separation strategies combined with novel quantitative MS methodologies have greatly improved analytical sensitivity, specificity, and throughput. This review summarizes current MS-based glycoproteomics approaches and highlights recent advances in its application to cancer biomarker and neurodegenerative disease research.
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Affiliation(s)
- Dustin C Frost
- School of Pharmacy, University of Wisconsin, Madison, Wisconsin, USA
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin, Madison, Wisconsin, USA; Department of Chemistry, University of Wisconsin, Madison, Wisconsin, USA.
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47
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Halim MA, MacAleese L, Lemoine J, Antoine R, Dugourd P, Girod M. Ultraviolet, Infrared, and High-Low Energy Photodissociation of Post-Translationally Modified Peptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:270-283. [PMID: 28980177 DOI: 10.1007/s13361-017-1794-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 08/17/2017] [Accepted: 08/18/2017] [Indexed: 06/07/2023]
Abstract
Mass spectrometry-based methods have made significant progress in characterizing post-translational modifications in peptides and proteins; however, certain aspects regarding fragmentation methods must still be improved. A good technique is expected to provide excellent sequence information, locate PTM sites, and retain the labile PTM groups. To address these issues, we investigate 10.6 μm IRMPD, 213 nm UVPD, and combined UV and IR photodissociation, known as HiLoPD (high-low photodissociation), for phospho-, sulfo-, and glyco-peptide cations. IRMPD shows excellent backbone fragmentation and produces equal numbers of N- and C-terminal ions. The results reveal that 213 nm UVPD and HiLoPD methods can provide diverse backbone fragmentation producing a/x, b/y, and c/z ions with excellent sequence coverage, locate PTM sites, and offer reasonable retention efficiency for phospho- and glyco-peptides. Excellent sequence coverage is achieved for sulfo-peptides and the position of the SO3 group can be pinpointed; however, widespread SO3 losses are detected irrespective of the methods used herein. Based on the overall performance achieved, we believe that 213 nm UVPD and HiLoPD can serve as alternative options to collision activation and electron transfer dissociations for phospho- and glyco-proteomics. Graphical Abstract ᅟ.
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Affiliation(s)
- Mohammad A Halim
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622, Lyon, France
| | - Luke MacAleese
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622, Lyon, France
| | - Jérôme Lemoine
- Université de Lyon, Institut des Sciences Analytiques, UMR 5280, CNRS, Université Lyon 1, ENS Lyon, 69622, Villeurbanne, Cedex, France
| | - Rodolphe Antoine
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622, Lyon, France
| | - Philippe Dugourd
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622, Lyon, France.
| | - Marion Girod
- Université de Lyon, Institut des Sciences Analytiques, UMR 5280, CNRS, Université Lyon 1, ENS Lyon, 69622, Villeurbanne, Cedex, France
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48
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Fang P, Wang XJ, Xue Y, Liu MQ, Zeng WF, Zhang Y, Zhang L, Gao X, Yan GQ, Yao J, Shen HL, Yang PY. In-depth mapping of the mouse brain N-glycoproteome reveals widespread N-glycosylation of diverse brain proteins. Oncotarget 2018; 7:38796-38809. [PMID: 27259237 PMCID: PMC5122430 DOI: 10.18632/oncotarget.9737] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 04/26/2016] [Indexed: 01/16/2023] Open
Abstract
N-glycosylation is one of the most prominent and abundant posttranslational modifications of proteins. It is estimated that over 50% of mammalian proteins undergo glycosylation. However, the analysis of N-glycoproteins has been limited by the available analytical technology. In this study, we comprehensively mapped the N-glycosylation sites in the mouse brain proteome by combining complementary methods, which included seven protease treatments, four enrichment techniques and two fractionation strategies. Altogether, 13492 N-glycopeptides containing 8386 N-glycosylation sites on 3982 proteins were identified. After evaluating the performance of the above methods, we proposed a simple and efficient workflow for large-scale N-glycosylation site mapping. The optimized workflow yielded 80% of the initially identified N-glycosylation sites with considerably less effort. Analysis of the identified N-glycoproteins revealed that many of the mouse brain proteins are N-glycosylated, including those proteins in critical pathways for nervous system development and neurological disease. Additionally, several important biomarkers of various diseases were found to be N-glycosylated. These data confirm that N-glycosylation is important in both physiological and pathological processes in the brain, and provide useful details about numerous N-glycosylation sites in brain proteins.
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Affiliation(s)
- Pan Fang
- Minhang Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Xin-Jian Wang
- State Key Laboratory of Medical Neurobiology, Institutes of Brain Science, and Collaborative Innovation Center for Brain Science, Fudan University, Shanghai, China
| | - Yu Xue
- Department of Chemistry, Fudan University, Shanghai, China
| | - Ming-Qi Liu
- Minhang Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Wen-Feng Zeng
- Key Laboratory of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS, Beijing, China
| | - Yang Zhang
- Minhang Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Lei Zhang
- Minhang Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Xing Gao
- Minhang Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Guo-Quan Yan
- Department of Chemistry, Fudan University, Shanghai, China
| | - Jun Yao
- Minhang Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Hua-Li Shen
- Minhang Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, China.,Department of Systems Biology for Medicine and School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Peng-Yuan Yang
- Minhang Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, China.,Department of Chemistry, Fudan University, Shanghai, China.,Department of Systems Biology for Medicine and School of Basic Medical Sciences, Fudan University, Shanghai, China
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49
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Patel S. A critical review on serine protease: Key immune manipulator and pathology mediator. Allergol Immunopathol (Madr) 2017; 45:579-591. [PMID: 28236540 PMCID: PMC7126602 DOI: 10.1016/j.aller.2016.10.011] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 10/31/2016] [Indexed: 11/29/2022]
Abstract
Proteolytic activity is fundamental to survival, so it is not surprising that all living organisms have proteases, especially seine protease. This enzyme in its numerous isoforms and homologues, constitutes the quintessential offence and defence factors, in the form of surface proteins, secreted molecules, gut digestive enzymes, venom in specialised glands or plant latex, among other manifestations. Occurring as trypsin, chymotrypsin, elastase, collagenase, thrombin, subtilisin etc., it mediates a diverse array of functions, including pathological roles as inflammatory, coagulatory to haemorrhagic. This review emphasizes that despite the superficial differences in mechanisms, most health issues, be they infectious, allergic, metabolic, or neural have a common conduit. This enzyme, in its various glycosylated forms leads to signal misinterpretations, wreaking havoc. However, organisms are endowed with serine protease inhibitors which might restrain this ubiquitous yet deleterious enzyme. Hence, serine proteases-driven pathogenesis and antagonising role of inhibitors is the focal point of this critical review.
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50
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Yang X, Wang Z, Guo L, Zhu Z, Zhang Y. Proteome-Wide Analysis of N-Glycosylation Stoichiometry Using SWATH Technology. J Proteome Res 2017; 16:3830-3840. [DOI: 10.1021/acs.jproteome.7b00480] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Xiangyun Yang
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhiyuan Wang
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lin Guo
- University of Chinese Academy of Sciences, Beijing 100049, China
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