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1.
Nat Methods ; 18(12): 1515-1523, 2021 12.
Article in English | MEDLINE | ID: mdl-34824474

ABSTRACT

Great advances have been made in mass spectrometric data interpretation for intact glycopeptide analysis. However, accurate identification of intact glycopeptides and modified saccharide units at the site-specific level and with fast speed remains challenging. Here, we present a glycan-first glycopeptide search engine, pGlyco3, to comprehensively analyze intact N- and O-glycopeptides, including glycopeptides with modified saccharide units. A glycan ion-indexing algorithm developed for glycan-first search makes pGlyco3 5-40 times faster than other glycoproteomic search engines without decreasing accuracy or sensitivity. By combining electron-based dissociation spectra, pGlyco3 integrates a dynamic programming-based algorithm termed pGlycoSite for site-specific glycan localization. Our evaluation shows that the site-specific glycan localization probabilities estimated by pGlycoSite are suitable to localize site-specific glycans. With pGlyco3, we confidently identified N-glycopeptides and O-mannose glycopeptides that were extensively modified by ammonia adducts in yeast samples. The freely available pGlyco3 is an accurate and flexible tool that can be used to identify glycopeptides and modified saccharide units.


Subject(s)
Computational Biology/methods , Glycopeptides/chemistry , Proteome , Proteomics/methods , Algorithms , Animals , Fireflies , Glycosylation , HEK293 Cells , Humans , Mannose/chemistry , Polysaccharides/chemistry , Probability , Reproducibility of Results , Saccharomyces cerevisiae , Schizosaccharomyces , Software
2.
Nat Methods ; 18(11): 1304-1316, 2021 11.
Article in English | MEDLINE | ID: mdl-34725484

ABSTRACT

Glycoproteomics is a powerful yet analytically challenging research tool. Software packages aiding the interpretation of complex glycopeptide tandem mass spectra have appeared, but their relative performance remains untested. Conducted through the HUPO Human Glycoproteomics Initiative, this community study, comprising both developers and users of glycoproteomics software, evaluates solutions for system-wide glycopeptide analysis. The same mass spectrometrybased glycoproteomics datasets from human serum were shared with participants and the relative team performance for N- and O-glycopeptide data analysis was comprehensively established by orthogonal performance tests. Although the results were variable, several high-performance glycoproteomics informatics strategies were identified. Deep analysis of the data revealed key performance-associated search parameters and led to recommendations for improved 'high-coverage' and 'high-accuracy' glycoproteomics search solutions. This study concludes that diverse software packages for comprehensive glycopeptide data analysis exist, points to several high-performance search strategies and specifies key variables that will guide future software developments and assist informatics decision-making in glycoproteomics.


Subject(s)
Glycopeptides/blood , Glycoproteins/blood , Informatics/methods , Proteome/analysis , Proteomics/methods , Research Personnel/statistics & numerical data , Software , Glycosylation , Humans , Proteome/metabolism , Tandem Mass Spectrometry
3.
Mol Cell Biochem ; 2024 Jan 31.
Article in English | MEDLINE | ID: mdl-38294731

ABSTRACT

Subdural hematoma (SDH) drains into the extracranial lymphatic system through the meningeal lymphatic vessels (mLVs) but the formation of SDH impairs mLVs. Because vitamin D (Vit D) can protect the endothelial cells, we hypothesized that Vit D may enhance the SDH clearance. SDH was induced in Sprague-Dawley rats and treated with Vit D or vehicle. Hematoma volume in each group was measured by H&E staining and hemoglobin quantification. Evans blue (EB) quantification and red blood cells injection were used to evaluated the drainage of mLVs. Western blot analysis and immunofluorescence were conducted to assess the expression of lymphatic protein markers. We also examined the inflammatory factors levels in subdural space by ELISA. Vit D treatment significantly reduced SDH volume and improved the drainage of SDH to cervical lymph nodes. The structure of mLVs in SDH rats were protected by Vit D, and the expressions of LYVE1, PROX1, FOXC2, and VE-cadherin were increased after Vit D treatment. The TNF-α, IL-6, and IL-8 levels were reduced in Vit D group. In vitro, Vit D also increased the VE-cadherin expression levels under inflammation. Vit D protects the structure of mLVs and enhances the absorption of SDH, partly by the anti-inflammatory effect of Vit D.

4.
World J Microbiol Biotechnol ; 40(6): 192, 2024 May 06.
Article in English | MEDLINE | ID: mdl-38709285

ABSTRACT

The global concern over arsenic contamination in water due to its natural occurrence and human activities has led to the development of innovative solutions for its detection and remediation. Microbial metabolism and mobilization play crucial roles in the global cycle of arsenic. Many microbial arsenic-resistance systems, especially the ars operons, prevalent in bacterial plasmids and genomes, play vital roles in arsenic resistance and are utilized as templates for designing synthetic bacteria. This review novelty focuses on the use of these tailored bacteria, engineered with ars operons, for arsenic biosensing and bioremediation. We discuss the advantages and disadvantages of using synthetic bacteria in arsenic pollution treatment. We highlight the importance of genetic circuit design, reporter development, and chassis cell optimization to improve biosensors' performance. Bacterial arsenic resistances involving several processes, such as uptake, transformation, and methylation, engineered in customized bacteria have been summarized for arsenic bioaccumulation, detoxification, and biosorption. In this review, we present recent insights on the use of synthetic bacteria designed with ars operons for developing tailored bacteria for controlling arsenic pollution, offering a promising avenue for future research and application in environmental protection.


Subject(s)
Arsenic , Bacteria , Biodegradation, Environmental , Biosensing Techniques , Operon , Biosensing Techniques/methods , Arsenic/metabolism , Bacteria/genetics , Bacteria/metabolism , Synthetic Biology/methods , Genetic Engineering
5.
Anal Chem ; 95(21): 8223-8231, 2023 05 30.
Article in English | MEDLINE | ID: mdl-37194568

ABSTRACT

Mass spectrometry-based glycome analysis is a viable strategy for the compositional and functional exploration of glycosylation. However, the lack of generic tools for high-throughput and reliable glycan spectral interpretation largely hampers the broad usability of glycomic research. Here, we developed a generic and reliable glycomic tool, GlycoNote, for comprehensive and precise glycome analysis. GlycoNote supports interpretation of tandem-mass spectrometry glycomic data from any sample source, uses a novel target-decoy method with iterative decoy searching for highly reliable result output, and embeds an open-search component analysis mode for heterogeneity analysis of monosaccharides and modifications. We tested GlycoNote on several different large-scale glycomic datasets, including human milk oligosaccharides, N- and O-glycome from human cell lines, plant polysaccharides, and atypical glycans from Caenorhabditis elegans, demonstrating its high capacity for glycome analysis. An application of GlycoNote to the analysis of labeled and derived glycans further demonstrates its broad usability in glycomic studies. By enabling generic characterization of various glycan types and elucidation of component heterogeneity in glycomic samples, the freely available GlycoNote is a promising tool for facilitating glycomics in glycobiology research.


Subject(s)
Glycomics , Polysaccharides/chemistry , Glycomics/methods , Humans , Tandem Mass Spectrometry
6.
Mol Cell Proteomics ; 20: 100060, 2021.
Article in English | MEDLINE | ID: mdl-33556625

ABSTRACT

Intact glycopeptide identification has long been known as a key and challenging barrier to the comprehensive and accurate understanding the role of glycosylation in an organism. Intact glycopeptide analysis is a blossoming field that has received increasing attention in recent years. MS-based strategies and relative software tools are major drivers that have greatly facilitated the analysis of intact glycopeptides, particularly intact N-glycopeptides. This article provides a systematic review of the intact glycopeptide-identification process using MS data generated in shotgun proteomic experiments, which typically focus on N-glycopeptide analysis. Particular attention is paid to the software tools that have been recently developed in the last decade for the interpretation and quality control of glycopeptide spectra acquired using different MS strategies. The review also provides information about the characteristics and applications of these software tools, discusses their advantages and disadvantages, and concludes with a discussion of outstanding tools.


Subject(s)
Glycopeptides/analysis , Software , Animals , Humans , Mass Spectrometry , Proteomics
7.
BMC Genomics ; 23(1): 665, 2022 Sep 21.
Article in English | MEDLINE | ID: mdl-36131263

ABSTRACT

BACKGROUND: Portal vein ligation (PVL)-induced liver hypertrophy increases future liver remnant (FLR) volume and improves resectability of large hepatic carcinoma. However, the molecular mechanism by which PVL facilitates liver hypertrophy remains poorly understood. METHODS: To gain mechanistic insight, we established a rat PVL model and carried out a comprehensive transcriptome analyses of hepatic lobes preserving portal blood supply at 0, 1, 7, and 14-day after PVL. The differentially expressed (DE) long-non coding RNAs (lncRNAs) and mRNAs were applied to conduct weighted gene co-expression network analysis (WGCNA). LncRNA-mRNA co-expression network was constructed in the most significant module. The modules and genes associated with PVL-induced liver hypertrophy were assessed through quantitative real-time PCR. RESULTS: A total of 4213 DElncRNAs and 6809 DEmRNAs probesets, identified by transcriptome analyses, were used to carry out WGCNA, by which 10 modules were generated. The largest and most significant module (marked in black_M6) was selected for further analysis. Gene Ontology (GO) analysis of the module exhibited several key biological processes associated with liver regeneration such as complement activation, IL-6 production, Wnt signaling pathway, autophagy, etc. Sixteen mRNAs (Notch1, Grb2, IL-4, Cops4, Stxbp1, Khdrbs2, Hdac2, Gnb3, Gng10, Tlr2, Sod1, Gosr2, Rbbp5, Map3k3, Golga2, and Rev3l) and ten lncRNAs (BC092620, AB190508, EF076772, BC088302, BC158675, BC100646, BC089934, L20987, BC091187, and M23890) were identified as hub genes in accordance with gene significance value, module membership value, protein-protein interaction (PPI) and lncRNA-mRNA co-expression network. Furthermore, the overexpression of 3 mRNAs (Notch1, Grb2 and IL-4) and 4 lncRNAs (BC089934, EF076772, BC092620, and BC088302) was validated in hypertrophic liver lobe tissues from PVL rats and patients undergoing hepatectomy after portal vein embolization (PVE). CONCLUSIONS: Microarray and WGCNA analysis revealed that the 3 mRNAs (Notch1, Grb2 and IL-4) and the 4 lncRNAs (BC089934, EF076772, BC092620 and BC088302) may be promising targets for accelerating liver regeneration before extensive hepatectomy.


Subject(s)
Liver Neoplasms , RNA, Long Noncoding , Animals , Hepatectomy , Hypertrophy , Interleukin-4 , Interleukin-6 , Liver/pathology , Liver/surgery , Liver Neoplasms/pathology , Liver Regeneration/genetics , Portal Vein/pathology , Portal Vein/surgery , RNA, Long Noncoding/genetics , RNA, Messenger/genetics , Rats , Superoxide Dismutase-1 , Toll-Like Receptor 2
8.
J Clin Lab Anal ; 36(10): e24706, 2022 Oct.
Article in English | MEDLINE | ID: mdl-36114782

ABSTRACT

BACKGROUND: Chronic subdural hematoma (CSDH) is a common neurosurgical disease with an increasing incidence. The absorption route of CSDH is not clear. Whether inflammatory factors enter the peripheral blood and cause systemic reactions is unknown. METHODS: We screened 105 CSDH patients and 105 control individuals. Their clinical characteristics and blood routine results were collected and compared. The blood routine changes of CSDH patients before and after treatment were compared. Age-stratified analysis was performed due to age may affect the inflammatory markers. RESULTS: The white blood cell count, absolute neutrophil count, neutrophil percentage, neutrophil-lymphocyte count ratio (NLR), and platelet to lymphocyte count ratio (PLR) of CSDH patients before treatment were within the normal range, while were significantly higher than the control individuals (p < 0.001). The absolute lymphocyte count and lymphocyte percentage of control individuals were higher than those of patients (p < 0.001). The inflammatory cells in patients of different age groups were similar. After the patient was cured, the white blood cell count, the absolute value and percentage of neutrophils decreased (p < 0.05), while the number of monocytes increased. CONCLUSIONS: CSDH caused slight systemic inflammatory responses in the peripheral blood, implying that there is a non-hematologic route for the absorption of hematoma.


Subject(s)
Hematoma, Subdural, Chronic , Hematoma, Subdural, Chronic/epidemiology , Hematoma, Subdural, Chronic/etiology , Hematoma, Subdural, Chronic/surgery , Humans , Leukocyte Count , Lymphocyte Count , Lymphocytes , Neutrophils , Retrospective Studies
9.
Anal Chem ; 93(17): 6682-6691, 2021 05 04.
Article in English | MEDLINE | ID: mdl-33877808

ABSTRACT

The heterogeneity and low abundance of protein glycosylation present challenging barriers to the analysis of intact glycopeptides, which is key to comprehensively understanding the role of glycosylation in an organism. Efficient and specific enrichment of intact glycopeptides could help greatly with this problem. Here, we propose a new enrichment strategy using a boronic acid (BA)-functionalized mesoporous graphene-silica composite (denoted as GO@mSiO2-GLYMO-APB) for isolating intact glycopeptides from complex biological samples. The merits of this composite, including high surface area and synergistic effect from size exclusion functionality of mesoporous material, hydrophilic interaction of silica, and the reversible covalent binding with BA, enable the effective and specific enrichment of both intact N- and O-glycopeptides. The results from the enrichment performance of the strategy evaluated by standard glycoproteins and the application to global N- and O-glycosylation analyses in human serum indicate the robustness and potential of the strategy for intact glycopeptide analysis.


Subject(s)
Graphite , Boronic Acids , Glycopeptides , Humans , Hydrophobic and Hydrophilic Interactions , Silicon Dioxide
10.
Neurol Sci ; 42(10): 4249-4255, 2021 Oct.
Article in English | MEDLINE | ID: mdl-33598798

ABSTRACT

BACKGROUNDS: Beta-2-microglobulin (ß2-MG) levels vary in many infectious and autoimmune diseases. We investigated plasma and cerebrospinal fluid (CSF) ß2-MG levels in patients with Guillain-Barré syndrome (GBS) and their correlations with clinical parameters. METHODS: CSF samples from 50 patients with GBS including 19 acute inflammatory demyelinating polyneuropathy (AIDP), 6 acute motor axonal neuropathy (AMAN), 10 acute motor-sensory axonal neuropathy (AMSAN), 7 Miller-Fisher syndrome (MFS), and 8 unclassified patients were collected. Moreover, 23 CSF samples from patients with non-inflammatory neurological disorders (NIND) as controls were collected. Plasma samples from 42 enrolled patients and 29 healthy individuals were also collected. The ß2-MG levels were measured by immunoturbidimetry on automatic biochemical analyser. Besides, clinical data were extracted from electronic patient documentation system. RESULTS: CSF levels of ß2-MG, lactate dehydrogenase (LDH), and lactate were significantly increased in patients with GBS (p = 0.004, p = 0.041, p = 0.040, respectively), particularly in patients with AIDP (p < 0.001, p = 0.001, p = 0.015, respectively), whereas no statistically significant difference was found in plasma levels of ß2-MG. Furthermore, CSF levels of ß2-MG were positively correlated with Hughes functional score (r = 0.493, p = 0.032), LDH (r = 0.796, p < 0.001), and lactate (r = 0.481, p = 0.037) but not with protein (r = - 0.090, p = 0.713) in AIDP patients. CONCLUSIONS: CSF ß2-MG levels may help identify AIDP and indicate clinical severity. CSF LDH and lactate levels correlate with CSF ß2-MG levels; interaction among these biomarkers would need further investigation.


Subject(s)
Guillain-Barre Syndrome , Miller Fisher Syndrome , Humans , beta 2-Microglobulin
11.
Mol Cell Proteomics ; 18(11): 2262-2272, 2019 11.
Article in English | MEDLINE | ID: mdl-31501225

ABSTRACT

N-glycosylation alteration has been reported in liver diseases. Characterizing N-glycopeptides that correspond to N-glycan structure with specific site information enables better understanding of the molecular pathogenesis of liver damage and cancer. Here, unbiased quantification of N-glycopeptides of a cluster of serum glycoproteins with 40-55 kDa molecular weight (40-kDa band) was investigated in hepatitis B virus (HBV)-related liver diseases. We used an N-glycopeptide method based on 18O/16O C-terminal labeling to obtain 82 comparisons of serum from patients with HBV-related hepatocellular carcinoma (HCC) and liver cirrhosis (LC). Then, multiple reaction monitoring (MRM) was performed to quantify N-glycopeptide relative to the protein content, especially in the healthy donor-HBV-LC-HCC cascade. TPLTAN205ITK (H5N5S1F1) and (H5N4S2F1) corresponding to the glycopeptides of IgA2 were significantly elevated in serum from patients with HBV infection and even higher in HBV-related LC patients, as compared with healthy donor. In contrast, the two glycopeptides of IgA2 fell back down in HBV-related HCC patients. In addition, the variation in the abundance of two glycopeptides was not caused by its protein concentration. The altered N-glycopeptides might be part of a unique glycan signature indicating an IgA-mediated mechanism and providing potential diagnostic clues in HBV-related liver diseases.


Subject(s)
Carcinoma, Hepatocellular/diagnosis , Glycopeptides/blood , Glycoproteins/blood , Hepatitis B/complications , Immunoglobulin A/blood , Liver Neoplasms/diagnosis , Proteome/analysis , Carcinoma, Hepatocellular/blood , Carcinoma, Hepatocellular/virology , Case-Control Studies , Glycosylation , Hepatitis B/virology , Hepatitis B virus/isolation & purification , Humans , Liver Neoplasms/blood , Liver Neoplasms/virology , Polysaccharides/metabolism
12.
Ann Nutr Metab ; 77(6): 313-323, 2021.
Article in English | MEDLINE | ID: mdl-34610596

ABSTRACT

BACKGROUND: Dietary interventions as a first-line treatment for patients with polycystic ovary syndrome (PCOS) have been evaluated, but the optimal diet has not been determined. Proper diet and the maintenance of adequate nutritional status are of great importance in the prevention of this disorder, and therapeutics and dietary habits play an important role in the recovery of patients with PCOS. SUMMARY: A range of dietary patterns have been shown to impact weight loss and insulin resistance (IR) and improve reproductive function, including the Mediterranean diet, the ketogenic diet, Dietary Approaches to Stop Hypertension, and other dietary patterns. Key Messages: Diets that can reduce rates of obesity and IR are beneficial to women with PCOS, the status of obesity and IR should be determined at the early stage of the disease, so as to develop individualized and sustainable dietary intervention. The long-term efficacy, safety, and health benefits of diet management in patients with PCOS need to be tested by further researches.


Subject(s)
Diet, Mediterranean , Insulin Resistance , Polycystic Ovary Syndrome , Female , Humans , Obesity/therapy , Polycystic Ovary Syndrome/therapy , Weight Loss
13.
Anal Chem ; 92(9): 6777-6784, 2020 05 05.
Article in English | MEDLINE | ID: mdl-32275135

ABSTRACT

Precise and automated analysis of site-specific O-glycosylation on single proteins is crucial for comprehensive characterization of some important glycoproteins, such as tumor biomarkers and recombinant drug proteins. Mass spectrometry has been proven to be a powerful technique for protein sequencing and N-glycosylation analysis. However, challenges remain in developing computational tools for intact O-glycopeptide analysis, which has greatly hindered the development of mass-spectrometry-based O-glycosylation analysis. Herein, an integrated strategy together with a dedicated automated computational tool termed AOGP was developed for intact O-glycopeptide analysis on single proteins. AOGP utilized de novo sequencing for O-glycans and a database search strategy for peptide backbones. The false discovery rate (FDR) of the identification results was controlled and validated by a mixed Gaussian distribution estimation method. AOGP exhibited superior performance in identifying intact O-glycopeptides of the human erythropoietin with a total of 188 O-glycopeptide spectra reported under 1% FDR. AOGP is developed in Python, is fully open-sourced, and is equipped with a user-friendly interface. Such an easy-operating and robust tool would greatly facilitate O-glycosylation analysis on single proteins in tumor biomarker and recombinant drug protein development.


Subject(s)
Algorithms , Asialoglycoproteins/analysis , Automation , Erythropoietin/analysis , Fetuins/analysis , Glycopeptides/analysis , Animals , Cattle , Glycosylation , Humans , Tandem Mass Spectrometry
14.
Anal Chem ; 92(1): 867-874, 2020 01 07.
Article in English | MEDLINE | ID: mdl-31751117

ABSTRACT

Protein N-glycosylation is ubiquitous in the brain and is closely related to cognition and memory. Alzheimer's disease (AD) is a multifactorial disorder that lacks a clear pathogenesis and treatment. Aberrant N-glycosylation has been suggested to be involved in AD pathology. However, the systematic variations in protein N-glycosylation and their roles in AD have not been thoroughly investigated due to technical challenges. Here, we applied multilayered N-glycoproteomics to quantify the global protein expression levels, N-glycosylation sites, N-glycans, and site-specific N-glycopeptides in AD (APP/PS1 transgenic) and wild-type mouse brains. The N-glycoproteomic landscape exhibited highly complex site-specific heterogeneity in AD mouse brains. The generally dysregulated N-glycosylation in AD, which involved proteins such as glutamate receptors as well as fucosylated and oligomannose glycans, were explored by quantitative analyses. Furthermore, functional studies revealed the crucial effects of N-glycosylation on proteins and neurons. Our work provides a systematic multilayered N-glycoproteomic strategy for AD and can be applied to diverse biological systems.


Subject(s)
Alzheimer Disease/metabolism , Brain/metabolism , Glycopeptides/metabolism , Glycoproteins/metabolism , Polysaccharides/metabolism , Animals , Brain Chemistry , Cell Line , Glycopeptides/analysis , Glycoproteins/chemistry , Glycosylation , Humans , Mice , Mice, Transgenic , Polysaccharides/analysis , Protein Processing, Post-Translational , Proteome/chemistry , Proteome/metabolism , Proteomics , Tandem Mass Spectrometry
16.
Expert Rev Proteomics ; 17(1): 11-25, 2020 01.
Article in English | MEDLINE | ID: mdl-31914820

ABSTRACT

Introduction: Glycomics, which aims to define the glycome of a biological system to better assess the biological attributes of the glycans, has attracted increasing interest. However, the complexity and diversity of glycans present challenging barriers to glycome definition. Technological advances are major drivers in glycomics.Areas covered: This review summarizes the main methods and emphasizes the most recent advances in mass spectrometry-based methods regarding glycomics following the general workflow in glycomic analysis.Expert opinion: Recent mass spectrometry-based technological advances have significantly lowered the barriers in glycomics. The field of glycomics is moving toward both generic and precise analysis.


Subject(s)
Glycomics/methods , Mass Spectrometry/methods , Animals , Humans , Polysaccharides/chemistry
17.
Mol Pharm ; 17(4): 1059-1070, 2020 04 06.
Article in English | MEDLINE | ID: mdl-31860321

ABSTRACT

Various types of nanocarriers modified with poly(ethylene glycol) (PEG) exhibit the accelerated blood clearance (ABC) phenomenon, resulting in reduced circulation time and abnormal increase in hepatic and splenic accumulations. Based on the abundance of esterases in the serum of rats, we developed cleavable methoxy PEG-cholesteryl methyl carbonate (mPEG-CHMC) with a carbonate linkage and noncleavable N-(carbonyl-methoxy PEG-n)-1,2-distearoyl-sn-glycero-3-phos-phoethanolamine (mPEG-DSPE) with a carbamate linkage on the surface of the nanoemulsions (CHMCE and PE, respectively). Both PEG derivatives possessed PEG with six different molecular weights (n = 350, 550, 750, 1000, 2000, and 5000). The pharmacokinetic behaviors and biodistributions of single and repeated injection of the two types of PEGylated nanoemulsions were determined to investigate the influence of cleavable linkages and PEG molecular weights on the ABC phenomenon in an attempt to find a potential strategy to eliminate the ABC phenomenon. CHMCEns (n = 1000, 2000, and 5000) exhibited the same pharmacokinetic behaviors as PE550 and PE750 and only alleviated the ABC phenomenon to a certain extent at the expense of shortened cycle time, indicating that the cleavable carbonate linkage was not an ideal strategy to eliminate the ABC phenomenon. As the molecular weights of PEG increased, the ABC phenomenon became more severe. Surprisingly, PE5000 induced a lower anti-PEG IgM level and a weaker ABC phenomenon compared with PE2000 while possessing a similar long circulation time. The results suggested that increasing the molecular weight of PEG in the PEG derivatives could be a potential strategy for eliminating the ABC phenomenon while simultaneously guaranteeing longer circulation time.


Subject(s)
Cholesterol/metabolism , Emulsions/metabolism , Lipids/chemistry , Nanoparticles/metabolism , Phospholipids/metabolism , Polyethylene Glycols/metabolism , Animals , Drug Carriers/chemistry , Drug Carriers/metabolism , Emulsions/chemistry , Immunoglobulin M/metabolism , Kinetics , Male , Metabolic Clearance Rate/physiology , Molecular Weight , Nanoparticles/chemistry , Polyethylene Glycols/chemistry , Rats , Rats, Wistar , Spleen/metabolism
18.
Anal Chem ; 91(19): 12435-12443, 2019 10 01.
Article in English | MEDLINE | ID: mdl-31453685

ABSTRACT

Efficient detection of aberrant glycoproteins in serum is particularly important for biomarker discovery. However, direct quantitation of glycoproteins in serum remains technically challenging because of the extraordinary complexity of the serum proteome. In the current work, we proposed a straightforward and highly efficient strategy by using the nonglycopeptides releasing from the specifically enriched glycoproteins for targeted glycoprotein quantification. With this so-called nonglycopeptide-based mass spectrometry (NGP-MS) strategy, a powerful and nondiscriminatory pipeline for hepatocellular carcinoma (HCC) glycoprotein biomarker discovery, verification, and validation has been developed. First, a data set of 234 NGPs was strictly established for multiple-reaction monitoring (MRM) quantification in serum. Second, the NGPs enriched from 20 HCC serum mixtures and 20 normal serum mixtures were labeled with mTRAQ reagents (Δ0 and Δ8, respectively) to find the differentially expressed glycoproteins in HCC. A total of 97 glycoprotein candidates were preliminarily screened and submitted for absolute quantitation with NGP-based stable-isotope-labeled (SID)-MRM in the individual samples of 38 HCC serum and 24 normal controls. Finally, 21 glycoproteins were absolutely quantified with high quality. The diagnostic sensitivity results showed that three glycoproteins, ß-2-glycoprotein 1 (APOH), α-1-acid glycoprotein 2 (ORM2), and complement C3 (C3), could be used for the discrimination between HCC patients and healthy people. A novel glycoprotein biomarker panel [APOH, ORM2, C3, and α-fetoprotein (AFP)] has proven to outperform AFP, the known HCC serum biomarker, alone, in this study. We believe that this strategy and the panel of glycoproteins might hold great clinical value for HCC detection in the future.


Subject(s)
Carcinoma, Hepatocellular/blood , Glycoproteins/blood , Liver Neoplasms/blood , Mass Spectrometry/methods , Biomarkers/blood , Humans , alpha-Fetoproteins/metabolism
19.
Protein Expr Purif ; 156: 17-24, 2019 04.
Article in English | MEDLINE | ID: mdl-30599198

ABSTRACT

The ricexip gene, which encodes the rice xylanase-inhibiting protein (riceXIP), was recombinantly expressed in Pichia pastoris GS115 under the control of AOX1 promoter. Recombinant riceXIP (rePriceXIP) was secreted into the supernatant and purified to homogeneity with the use of Ni-affinity resin. The molecular mass of rePriceXIP was approximately 44.0 kDa. RePriceXIP significantly inhibited the activity of GH11 xylanases in a concentration-dependent manner. The optimal inhibitory activity of rePriceXIP on GH11 xylanases (TfxA_CD214, reBaxA454, and TfxA_CD526) occurred at 40 °C for 30 min. The IC50 values of rePriceXIP inhibiting TfxA_CD214, reBaxA454, and TfxA_CD526 (0.5 U) were 45, 40, and 40 nM, respectively. The Ki of rePriceXIP on TfxA_CD214 xylanase was 12.2 nM. Increasing the concentration of rePriceXIP did not change Vmax, but increased Km, thereby suggesting that the inhibition was competitive. Analysis of the fluorescence intensities revealed that the Kq values for TfxA_CD214, reBaxA454, and TfxA_CD526 exceeded 2.0 × 1010 L mol-1•s-1, implying that static quenching occurred. Circular dichroism spectroscopy demonstrated that rePriceXIP bound to xylanase, thereby changing the secondary structure and reducing the catalytic activity of xylanase. Lower levels of hydrolytes are released from beechwood xylan by xylanases in the presence of rePriceXIP.


Subject(s)
Endo-1,4-beta Xylanases/antagonists & inhibitors , Enzyme Inhibitors/pharmacology , Oryza/enzymology , Recombinant Proteins/pharmacology , Aldehyde Oxidase/metabolism , Binding, Competitive , Hydrogen-Ion Concentration , Oryza/chemistry , Promoter Regions, Genetic , Recombinant Proteins/genetics
20.
Pharm Res ; 36(12): 176, 2019 Nov 04.
Article in English | MEDLINE | ID: mdl-31686241

ABSTRACT

PURPOSE: This study aimed to explore the potential of sialic acid - related selectin targeting strategy in the treatment of leukemia and some solid tumors. We expected it could "actively" bind tumor cells and kill them, reducing non-specific toxicity to normal cells. METHODS: BOR-SA prodrug was synthesized by reacting an ortho-dihydroxy group in SA with a boronic acid group in BOR. Two kinds of leukemia cells (RAW264.7 and HL60 cells), one solid sarcoma cell model (S180 cells) and their corresponding normal cells (monocytes (MO), neutrophil (NE) and fibroblast (L929)) were selected for the in vitro cell experiments (cytotoxicity, cellular uptake, cell cycle and apoptosis experiments). The S180 tumor-bearing Kunming mice model was established for anti-tumor pharmacodynamic experiments. RESULTS: In vitro cell assay results showed that uptake of BOR-SA by HL60 and S180 cells were increased compared with the control group. BOR-SA induced a lower IC50, higher ratio of apoptosis and cell cycle arrest of tumor cells. In vivo anti-S180 tumor pharmacodynamics experiments showed that mice in the BOR-SA group had higher tumor inhibition rate, higher body weight and lower immune organ toxicity compared with the control group. CONCLUSIONS: sialic acid-mediated selectin targeting strategy may have great potential in the treatment of related tumors.


Subject(s)
Antineoplastic Agents/pharmacokinetics , Bortezomib/pharmacokinetics , Leukemia/drug therapy , N-Acetylneuraminic Acid/chemistry , Prodrugs/pharmacokinetics , Selectins/metabolism , Animals , Antineoplastic Agents/administration & dosage , Antineoplastic Agents/chemical synthesis , Apoptosis/drug effects , Bortezomib/administration & dosage , Bortezomib/chemical synthesis , Cell Line, Tumor , Cell Membrane Permeability , Cell Proliferation/drug effects , Cell Survival/drug effects , Dose-Response Relationship, Drug , Humans , Male , Mannitol/chemistry , Mannitol/metabolism , Mice , Molecular Targeted Therapy/methods , N-Acetylneuraminic Acid/metabolism , Prodrugs/administration & dosage , Prodrugs/chemical synthesis , Selectins/genetics
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