Academic literature on the topic 'Glycan node analysis'
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Journal articles on the topic "Glycan node analysis"
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Walker, Sierra A., Jesús S. Aguilar Díaz De león, Sara Busatto, Gregory A. Wurtz, Abba C. Zubair, Chad R. Borges, and Joy Wolfram. "Glycan Node Analysis of Plasma-Derived Extracellular Vesicles." Cells 9, no. 9 (August 22, 2020): 1946. http://dx.doi.org/10.3390/cells9091946.
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Blood plasma is a readily accessible source of extracellular vesicles (EVs), i.e., cell-secreted nanosized carriers that contain various biomolecules, including glycans. Previous studies have demonstrated that glycans play a major role in physiological and pathological processes, and certain plasma glycans have been associated with disease conditions. However, glycome studies have been limited by a lack of analytical techniques with the throughput capacity necessary to study hundreds of clinical samples. This study is the first to characterize the EV plasma glycome based on all major glycan classes. The results based on glycan node analysis revealed, as expected, that plasma-derived EVs have distinct glycan features from donor-matched whole plasma. Specifically, glycan nodes corresponding to those observed in chondroitin sulfate, dermatan sulfate, type I keratan sulfate, and type II keratan sulfate were enriched on EVs. The identification of specific differences in glycan features in plasma vs. plasma-derived EVs is relevant for understanding the physiological role of EVs and as a reference for future diagnostic studies. Additionally, the results indicate that EV glycan nodes do not substantially differ among a small set of healthy donors. These results lay the framework for the further evaluation of all EV glycan classes as diagnostic markers, therapeutic targets, and biologically active components in health and disease.
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Ueno, Takayuki, Fumiaki Sato, Nobuhiko Shinkura, Taichi Aihara, Masao Fukushima, Masaru Sekijima, and Masakazu Toi. "Comprehensive analysis of serum N-glycans as a biomarker for breast cancer." Journal of Clinical Oncology 30, no. 15_suppl (May 20, 2012): e21031-e21031. http://dx.doi.org/10.1200/jco.2012.30.15_suppl.e21031.
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e21031 Background: Early detection of breast cancer is an important aspect to improve therapeutic outcome. Serum biomarkers have a number of advantages including less invasiveness and possible application for monitoring. Glycans are involved in many biological processes including cancer progression and promising candidates for cancer biomarker. Methods: Sera were collected from 54 patients with operable breast cancer and 118 healthy volunteers. N-glycans were isolated by BlotGlyco (Sumitomo Bakelite Co., LTD, Japan) and N-glycan profile was obtained by MALDI-TOF MS. The principal component analysis (PCA) was performed by SIMCA-P+ ver.12 (Umetrics). N-glycan compositions were estimated from mass spectra using 'GlycoMod' database. Results: Fifty-four pts (age: 31-78) and 118 healthy females (age: 29-73) were enrolled. The tumor size was between 9 and 107mm (median 29mm). Twenty six pts (48%) had lymph node involvement. Fifty three peaks of N-glycans were observed in more than 95% of the samples and utilized for the analyses. By PCA, no distinction was observed in sera form breast cancer pts in terms of the tumor size, hormone receptor status and HER2 status. The N-glycan signature to identify cancer pts was created based on the PCA. The signature categorized samples into three groups: cancer, healthy and border groups. Half of the samples (even registration number) were used for training and the rest for validation. In the validation cohort, 18 (66.7%) of 27 pts were categorized into the cancer group and 9 were into the border group. Forty-seven (79.7%) of 59 volunteers were categorized into the healthy group and 11 were into the border group. When the border group was included in the cancer group, the sensitivity was 100% (27 of 27 pts in the cancer group) and the specificity was 79.7% (47 of 59 volunteers in the healthy group). Conclusions: The comprehensive analysis of N-glycans in sera enabled the creation of the N-glycan signature to distinguish between breast cancer pts and healthy females with high sensitivity and high specificity. Confirmative studies are warranted.
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Herrera, Harmin, Tinslee Dilday, Allison Uber, Danielle Scott, Joelle N. Zambrano, Mengjun Wang, Peggi M. Angel, et al. "Core-Fucosylated Tetra-Antennary N-Glycan Containing A Single N-Acetyllactosamine Branch Is Associated with Poor Survival Outcome in Breast Cancer." International Journal of Molecular Sciences 20, no. 10 (May 23, 2019): 2528. http://dx.doi.org/10.3390/ijms20102528.
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(1) Glycoproteins account for ~80% of proteins located at the cell surface and in the extracellular matrix. A growing body of evidence indicates that α-L-fucose protein modifications contribute to breast cancer progression and metastatic disease. (2) Using a combination of techniques, including matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI-IMS) based in cell and on tissue imaging and glycan sequencing using exoglycosidase analysis coupled to hydrophilic interaction ultra-high performance liquid chromatography (HILIC UPLC), we establish that a core-fucosylated tetra-antennary glycan containing a single N-acetyllactosamine (F(6)A4G4Lac1) is associated with poor clinical outcomes in breast cancer, including lymph node metastasis, recurrent disease, and reduced survival. (3) This study is the first to identify a single N-glycan, F(6)A4G4Lac1, as having a correlation with poor clinical outcomes in breast cancer.
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Smit, Cornelis H., Christiaan L. Kies, Hamish E. G. McWilliam, Els N. T. Meeusen, Cornelis H. Hokke, and Angela van Diepen. "Local Antiglycan Antibody Responses to Skin Stage and Migratory Schistosomula of Schistosoma japonicum." Infection and Immunity 84, no. 1 (October 12, 2015): 21–33. http://dx.doi.org/10.1128/iai.00954-15.
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Schistosomiasis is a tropical disease affecting over 230 million people worldwide. Although effective drug treatment is available, reinfections are common, and development of immunity is slow. Most antibodies raised during schistosome infection are directed against glycans, some of which are thought to be protective. Developing schistosomula are considered most vulnerable to immune attack, and better understanding of local antibody responses raised against glycans expressed by this life stage might reveal possible glycan vaccine candidates for future vaccine research. We used antibody-secreting cell (ASC) probes to characterize local antiglycan antibody responses against migratingSchistosoma japonicumschistosomula in different tissues of rats. Analysis by shotgunSchistosomaglycan microarray resulted in the identification of antiglycan antibody response patterns that reflected the migratory pathway of schistosomula. Antibodies raised by skin lymph node (LN) ASC probes mainly targeted N-glycans with terminal mannose residues, Galβ1-4GlcNAc (LacNAc) and Galβ1-4(Fucα1-3)GlcNAc (LeX). Also, responses to antigenic and schistosome-specific glycosphingolipid (GSL) glycans containing highly fucosylated GalNAcβ1-4(GlcNAcβ1)nstretches that are believed to be present at the parasite's surface constitutively upon transformation were found. Antibody targets recognized by lung LN ASC probes were mainly N-glycans presenting GalNAcβ1-4GlcNAc (LDN) and GlcNAc motifs. Surprisingly, antibodies against highly antigenic multifucosylated motifs of GSL glycans were not observed in lung LN ASC probes, indicating that these antigens are not expressed in lung stage schistosomula or are not appropriately exposed to induce immune responses locally. The local antiglycan responses observed in this study highlight the stage- and tissue-specific expression of antigenic parasite glycans and provide insights into glycan targets possibly involved in resistance toS. japonicuminfection.
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Sun, In-Cheol, SeongHoon Jo, Diego Dumani, Wan Su Yun, Hong Yeol Yoon, Dong-Kwon Lim, Cheol-Hee Ahn, Stanislav Emelianov, and Kwangmeyung Kim. "Theragnostic Glycol Chitosan-Conjugated Gold Nanoparticles for Photoacoustic Imaging of Regional Lymph Nodes and Delivering Tumor Antigen to Lymph Nodes." Nanomaterials 11, no. 7 (June 28, 2021): 1700. http://dx.doi.org/10.3390/nano11071700.
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Lymph node mapping is important in cancer immunotherapy because the morphology of lymph nodes is one of the crucial evaluation criteria of immune responses. We developed new theragnostic glycol-chitosan-coated gold nanoparticles (GC-AuNPs), which highlighted lymph nodes in ultrasound-guided photoacoustic (US/PA) imaging. Moreover, the ovalbumin epitope was conjugated GC-AuNPs (OVA-GC-AuNPs) for delivering tumor antigen to lymph node resident macrophage. In vitro studies proved the vigorous endocytosis activity of J774A.1 macrophage and consequent strong photoacoustic signals from them. The macrophages also presented a tumor antigen when OVA-GC-AuNPs were used for cellular uptake. After the lingual injection of GC-AuNPs into healthy mice, cervical lymph nodes were visible in a US/PA imaging system with high contrast. Three-dimensional analysis of lymph nodes revealed that the accumulation of GC-AuNPs in the lymph node increased as the post-injection time passed. Histological analysis showed GC-AuNPs or OVA-GC-AuNPs located in subcapsular and medullar sinuses where macrophages are abundant. Our new theragnostic GC-AuNPs present a superior performance in US/PA imaging of lymph nodes without targeting moieties or complex surface modification. Simultaneously, GC-AuNPs were able to deliver tumor antigens to cause macrophages to present the OVA epitope at targeted lymph nodes, which would be valuable for cancer immunotherapy.
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Pratheek, H. P., N. Manikanta, K. S. Shashidhara, and M. S. P. Kanavi. "In-silico Analysis of Evolution of Plant Polyamine Oxidases." Research Journal of Biotechnology 16, no. 8 (July 25, 2021): 11–21. http://dx.doi.org/10.25303/168rjbt1121.
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Amino oxidase enzymes have attractive role in programmed cell death. Full length amino acid sequences of 46 polyamino oxidases (PAO) and 8 diamino oxidases (DAO) were retrieved from major sequence repositories. Sequences were obtained using combination of queries based on key terms and BLASTp searches. The PAOs belong to 21 and DAOs belong to 5 families. Multiple sequence alignment of amino-acid sequences identified the conserved residues to be Glycine, Glutamic acid, Alanine, Arginine, Tryptophan, Proline, Valine, Leucine, Phenylalanine, Tyrosine and Lysine. Glycine is most conserved followed by glutamic acid and proline. The phylogenetic analysis revealed the three main nodes/clades A, B and C. Clade C containing highest number of PAO species was followed by clade B. Clade A mostly contains tree species PAOs. Similar trend has been observed for DAOs. PAO and DAO genes of plants including Arabidopsis thaliana, Brachipodium, Glycin max, Oryza sativa present on different chromosomes. Comparative modelling was done to build 3D structure of the PAO and DAO from A. thaliana. In the Ramachandran plot, more than 90% residues were in most allowed regions. DAOs are mostly located in lysosomes and vacuoles in the cell and are in soluble form. PAOs located in cytoplasm and peroxisomes are in soluble form.
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Zou, Hang, Ni-Na Zhang, Qing Pan, Jian-Hua Zhang, Juan Chen, and Ge-Hong Wei. "Hydrogen Sulfide Promotes Nodulation and Nitrogen Fixation in Soybean–Rhizobia Symbiotic System." Molecular Plant-Microbe Interactions® 32, no. 8 (August 2019): 972–85. http://dx.doi.org/10.1094/mpmi-01-19-0003-r.
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The rhizobium–legume symbiotic system is crucial for nitrogen cycle balance in agriculture. Hydrogen sulfide (H2S), a gaseous signaling molecule, may regulate various physiological processes in plants. However, whether H2S has regulatory effect in this symbiotic system remains unknown. Herein, we investigated the possible role of H2S in the symbiosis between soybean (Glycine max) and rhizobium (Sinorhizobium fredii). Our results demonstrated that an exogenous H2S donor (sodium hydrosulfide [NaHS]) treatment promoted soybean growth, nodulation, and nitrogenase (Nase) activity. Western blotting analysis revealed that the abundance of Nase component nifH was increased by NaHS treatment in nodules. Quantitative real-time polymerase chain reaction data showed that NaHS treatment upregulated the expressions of symbiosis-related genes nodA, nodC, and nodD of S. fredii. In addition, expression of soybean nodulation marker genes, including early nodulin 40 (GmENOD40), ERF required for nodulation (GmERN), nodulation signaling pathway 2b (GmNSP2b), and nodulation inception genes (GmNIN1a, GmNIN2a, and GmNIN2b), were upregulated. Moreover, the expressions of glutamate synthase (GmGOGAT), asparagine synthase (GmAS), nitrite reductase (GmNiR), ammonia transporter (GmSAT1), leghemoglobin (GmLb), and nifH involved in nitrogen metabolism were upregulated in NaHS-treated soybean roots and nodules. Together, our results suggested that H2S may act as a positive signaling molecule in the soybean–rhizobia symbiotic system and enhance the system’s nitrogen fixation ability.
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Saeed, Anwaar Mohammed, Ammar Ali Alkhazna, Betty Herndon, and Daniel Dim. "Triggers in the pathway from lung cell damage to malignancy: The glycans." Journal of Clinical Oncology 31, no. 15_suppl (May 20, 2013): e22189-e22189. http://dx.doi.org/10.1200/jco.2013.31.15_suppl.e22189.
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e22189 Background: It has been reported that carbon nanoparticles (CN) produce mesothelioma as readily as do asbestos fibers. We have studied early CN damage in experimental animals, quantifying toxicity by release from cells of the nuclear chaperone HMGB1. Damage-released HMGB1 binds to receptors (RAGE, CD24) to upregulate cytokines and produce regulatory signals that control cell homeostasis. Further, HMGB1 has recently been shown to form a complex with P53, one of the most commonly mutated genes in human cancers, and HMGB1 is the controlling factor in autophagy, an important new field in translational cancer research. Methods: One HMGB1 receptor, CD24, is the source of a whole-receptor antibody used to determine extent of malignancy during surgery. CD24 is highly glycosylated. We hypothesized that carbohydrate vs protein specificity would show differences in tumor character. Would antibodies to the CD24 carbohydrate moiety reflect a tumor glycan character, and how would this relate to the tumor profile such as metastasis? With cooperation of TMC pathology Dept, blocks (N=15 each) of lung squamous cell, adenocarcinoma, and small cell cancer were sectioned and stained with mouse monoclonals to CD24, IgM –glycan, IgG-protein fraction. Results: Small cell and adenocarcinoma lung tumors showed mostly similar staining by CD24 protein vs CD24 glycan antibodies. Squamous cell CA showed elevated carbohydrate CD24 staining with negative or low protein stain in over half of the cases, and examination of patient records are being studied to determine metastatic character, lung- damage history and tumor chemotherapy response. Conclusions: Squamous cell tumors demonstrate significantly more staining by antibody to the glycan moiety of CD24, p=0.02. There was no relationship between numbers of positive nodes and staining, although other chart information awaits analysis. Research continues into the significance of this glycan CD24 receptor for HMGB1, our marker for nanoparticle lung damage, and its relationship to malignant transformation. [Table: see text]
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Scheel, Julia, and Detlef Keller. "Investigation of the Skin Sensitizing Properties of 5 Osmolytic Prodrugs in a Weight-of-Evidence Assessment, Employing In Silico, In Vivo, and Read Across Analyses." International Journal of Toxicology 31, no. 4 (July 31, 2012): 358–63. http://dx.doi.org/10.1177/1091581812449662.
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The amino acid esters ethyl glycinate (EG), dl-α-tocopheryl-(mono-)betainate hydrochloride (TMB), dl-α-tocopheryl-(mono-)glycinate hydrochloride (TMG), dl-α-tocopheryl-(mono-)prolinate hydrochloride (TMP), and dl-α-tocopheryl-(mono-)sarcosinate hydrochloride (TMS) were previously shown to exert an osmoprotective function to human skin in vitro. Based on literature data, the parent compounds α-tocopherol (vitamin E) and the amino acids glycine, betaine (trimethylated glycine), proline, and sarcosine ( N-methylated glycine) are not considered to be sensitizers. To investigate skin sensitizing properties of the esters, EG, TMG, and TMP were tested in the Local Lymph Node Assay (LLNA). Remaining esters were assessed by read across analysis considering structural similarities and mechanistic aspects. The LLNA results were consistent with in silico outcomes from ToxTree 2.5.0 indicative for protein binding; EG was negative; TMG and TMP were positive. Since TMB and TMS showed structural similarities to TMG and TMP and were also positive in ToxTree, it was concluded that both TMB and TMS can also be expected to have a skin sensitizing potential and therefore animal testing was waived.
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Car, Iris, Sarah Visentin, Davorin Đanić, and Marko Klobučar. "Different expression of lumican glycoforms in non-metastatic and metastatic laryngeal squamous cell carcinoma." Medicina Fluminensis 57, no. 1 (March 1, 2021): 114–21. http://dx.doi.org/10.21860/medflum2021_365329.
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Objective: Association of altered growth factor receptors-mediated intracellular pathways and biological processes associated with extracellular matrix composition and structure in laryngeal squamous cell carcinoma (LSCC) were described previously. In particular, the expression and glycosylation of important extracellular matrix molecules (ECM) such as small leucine rich proteoglycan lumican, may be generally associated with disrupted extracellular matrix integrity and inflammation processes which have a role in tumour invasiveness. In this study, the relative expression of different lumican glycoforms were evaluated in primary tumour and tumour-unaffected tissue samples of ten patients with metastatic and ten non-metastatic LSCC by Western blot and 2D immunoblot analysis. Materials and methods: Tissue samples from the primary tumours and paired adjacent non-tumour tissues were surgically resected from ten untreated LSCC patients with non-metastatic disease and ten LSCC patients with lymph nodes metastases. The relative expression of different lumican glycoforms in primary tumours and paired adjacent non-tumour tissues were evaluated by Western blot and 2D immunoblot analysis. Results: Results of Western blot analysis have revealed elevated expression of the moderately glycosylated lumican form in metastatic (p<0,05) and non-metastatic primary tumour tissues in comparison with tumour unaffected tissues. In addition, moderately glycosylated form of lumican with negatively charged oligosaccharide residues in the N-glycan molecule part was exclusively determined in metastatic primary tumour tissues by 2D immunoblot analysis. Conclusion: We demonstrated elevated expression of the moderately glycosylated lumican form with negatively charged oligosaccharide residues in the N-glycan portion exclusively in primary laryngeal squamous cell carcinoma from patients with metastatic disease.
Dissertations / Theses on the topic "Glycan node analysis"
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"Blood Plasma-Based Glycan Nodes as Lung Cancer Markers and the Problem of Biospecimen Integrity in a Multi-Site Clinical Study." Doctoral diss., 2019. http://hdl.handle.net/2286/R.I.53744.
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abstract: Cancer is a major public health challenge and the second leading cause of death in the United States. Large amount of effort has been made to achieve sensitive and specific detection of cancer, and to predict the course of cancer. Glycans are promising avenues toward the diagnosis and prognosis of cancer, because aberrant glycosylation is a prevalent hallmark of diverse types of cancer. A bottom-up “glycan node analysis” approach was employed as a useful tool, which captures most essential glycan features from blood plasma or serum (P/S) specimens and quantifies them as single analytical signals, to a lung cancer set from the Women Epidemiology Lung Cancer (WELCA) study. In addition, developments were performed to simplify a relatively cumbersome step involved in sample preparation of glycan node analysis. Furthermore, as a biomarker discovery research, one crucial concern of the glycan node analysis is to ensure that the specimen integrity has not been compromised for the employed P/S samples. A simple P/S integrity quality assurance assay was applied to the same sample set from WELCA study, which also afford the opportunity to evaluate the effects of different collection sites on sample integrity in a multisite clinical trial.
Here, 208 samples from lung cancer patients and 207 age-matched controls enrolled in the WELCA study were analyzed by glycan node analysis. Glycan features, quantified as single analytical signals, including 2-linked mannose, α2‐6 sialylation, β1‐4 branching, β1‐6 branching, 4-linked GlcNAc, and outer-arm fucosylation, exhibited abilities to distinguish lung cancer cases from controls and predict survival in patients.
To circumvent the laborious preparation steps for permethylation of glycan node analysis, a spin column-free (SCF) glycan permethylation procedure was developed, applicable to both intact glycan analysis or glycan node analysis, with improved or comparable permethylation efficiency relative to some widely-used spin column-based procedures.
Biospecimen integrity of the same set of plasma samples from WELCA study was evaluated by a simple intact protein assay (ΔS-Cysteinylated-Albumin), which quantifies cumulative exposure of P/S to thawed conditions (-30 °C). Notable differences were observed between different groups of samples with various initial handling/storage conditions, as well as among the different collection sites.Dissertation/Thesis
Doctoral Dissertation Biochemistry 2019
Book chapters on the topic "Glycan node analysis"
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Aguilar Díaz de león, Jesús S., and Chad R. Borges. "Glycosylation Profiling of Glycoproteins Secreted from Cultured Cells Using Glycan Node Analysis and GC-MS." In Methods in Molecular Biology, 317–30. New York, NY: Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1241-5_22.
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