Glycomic analysis using KEGG GLYCAN

Carbohydrate Structure Database: current state and recent developments

Carbohydrate Structure Database (CSDB) is a curated glycan data collection and a glycoinformatic platform. In this report, its database, analytical, and other components that have appeared for the recent years are reviewed. The major improvements were achieving close-to-full coverage on glycans from microorganisms, launching modules for glycosyltransferases and saccharide conformations, online glycan builder and 3D modeler, NMR simulator, NMR-based structure predictor, and other tools.

Source files of the Carbohydrate Structure Database: the way to sophisticated analysis of natural glycans

The Carbohydrate Structure Database (CSDB, http://csdb.glycoscience.ru/ ) is a free curated repository storing various data on glycans of bacterial, fungal and plant origins. Currently, it maintains a close-to-full coverage on bacterial and fungal carbohydrates up to the year 2020. The CSDB web-interface provides free access to the database content and dedicated tools. Still, the number of these tools and the types of the corresponding analyses is limited, whereas the database itself contains data that can be used in a broader scope of analytical studies. In this paper, we present CSDB source data files and a self-contained SQL dump, and exemplify their possible application in glycan-related studies. By using CSDB in an SQL format, the user can gain access to the chain length distribution or charge distribution (as an example) in a given set of glycans defined according to specific structural, taxonomic, or other parameters, whereas the source text dump files can be imported to any dedicated database with a specific internal architecture differing from that of CSDB.

ANALYSIS OF CARBOHYDRATES AND GLYCOCONJUGATES BY MATRIX-ASSISTED LASER DESORPTION/IONIZATION MASS SPECTROMETRY: AN UPDATE FOR 2015-2016

This review is the ninth update of the original article published in 1999 on the application of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2016. Also included are papers that describe methods appropriate to analysis by MALDI, such as sample preparation techniques, even though the ionization method is not MALDI. Topics covered in the first part of the review include general aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, fragmentation and arrays. The second part of the review is devoted to applications to various structural types such as oligo- and poly-saccharides, glycoproteins, glycolipids, glycosides and biopharmaceuticals. Much of this material is presented in tabular form. The third part of the review covers medical and industrial applications of the technique, studies of enzyme reactions and applications to chemical synthesis. The reported work shows increasing use of combined new techniques such as ion mobility and the enormous impact that MALDI imaging is having. MALDI, although invented over 30 years ago is still an ideal technique for carbohydrate analysis and advancements in the technique and range of applications show no sign of deminishing. © 2020 Wiley Periodicals, Inc.

Emerging glycobiology tools: A renaissance in accessibility

The glycobiology of the immune response is a topic that has garnered increased attention due to a number of key discoveries surrounding IgG function, the specificity of some broadly neutralizing anti-HIV antibodies, cancer immunoregulation by galectin molecules and others. This review is the opening article in a Special Edition of Cellular Immunology focused on glycoimmunology, and has the goal of setting the context for these articles by providing a mini-review of how glycans impact immunity. We also focus on some of the technological and methodological advances in the field of glycobiology that are being deployed to lower the barrier of entry into the glycosciences, and to more fully interrogate the glycome and its function.

Screening of genes involved in epithelial-mesenchymal transition and differential expression of complement-related genes induced by PAX2 in renal tubules

Aim

The aim of the present study was to screen and verify downstream genes involved in the epithelial mesenchymal transition (EMT) induced by paired box 2 (PAX2) in NRK‐52E cells.

Methods

NRK‐52E cells were transfected with lentivirus carrying PAX2 gene or no‐load virus respectively. Total RNA was isolated 72 h after transfection from PAX2‐overexpressing cells and control cells. Isolated RNA was then hybridized with the Rat OneArray Plus expression profile chip. The chips were examined by Agilent 0.1 XDR to screen for differentially expressed genes, which were further analyzed to investigate complement‐related genes as genes of interest.

Results

In NRK‐52E cells, PAX2 overexpression promoted EMT followed by upregulation of 298 genes and downregulation of 293 genes. KEGG analysis indicated the differential expression of genes related to cytokines and their receptors, extracellular matrix (ECM), MAPKs, local adhesion, cancer, the complement cascade, and coagulation. Gene oncology analysis screened out genes related to molecular functions (e.g., hydrolase activity, phospholipase activity, components of the ECM) and biological processes (e.g., cell development, signal transduction, phylogeny), and cell components (e.g., cytoplasm, cell membrane, and ECM). Analysis of the complement system revealed upregulation of C3 and downregulation of CD55 and complement regulator factor H (CFH).

Conclusion

PAX2 overexpression upregulates EMT in vitro and may regulate C3, CD55, and CFH.

This molecular analysis examines the effect of overexpressing paired box 2 (PAX2) in a tubule epithelial cell line. Results establish a link between pax2 and both epithelial‐mesenchymal transition (EMT) and the complement pathway.

Bacterial Glycoengineering as a Biosynthetic Route to Customized Glycomolecules

Bacteria have garnered increased interest in recent years as a platform for the biosynthesis of a variety of glycomolecules such as soluble oligosaccharides, surface-exposed carbohydrates, and glycoproteins. The ability to engineer commonly used laboratory species such as Escherichia coli to efficiently synthesize non-native sugar structures by recombinant expression of enzymes from various carbohydrate biosynthesis pathways has allowed for the facile generation of important products such as conjugate vaccines, glycosylated outer membrane vesicles, and a variety of other research reagents for studying and understanding the role of glycans in living systems. This chapter highlights some of the key discoveries and technologies for equipping bacteria with the requisite biosynthetic machinery to generate such products. As the bacterial glyco-toolbox continues to grow, these technologies are expected to expand the range of glycomolecules produced recombinantly in bacterial systems, thereby opening up this platform to an even larger number of applications.

Two-Dimensional N-Glycan Distribution Mapping of Hepatocellular Carcinoma Tissues by MALDI-Imaging Mass Spectrometry

A new mass spectrometry imaging approach to simultaneously map the two-dimensional distribution of N-glycans in tissues has been recently developed. The method uses Matrix Assisted Laser Desorption Ionization Imaging Mass Spectrometry (MALDI-IMS) to spatially profile the location and distribution of multiple N-linked glycan species released by peptide N-glycosidase F in frozen or formalin-fixed tissues. Multiple formalin-fixed human hepatocellular carcinoma tissues were evaluated with this method, resulting in a panel of over 30 N-glycans detected. An ethylation reaction of extracted N-glycans released from adjacent slides was done to stabilize sialic acid containing glycans, and these structures were compared to N-glycans detected directly from tissue profiling. In addition, the distribution of singly fucosylated N-glycans detected in tumor tissue microarray cores were compared to the histochemistry staining pattern of a core fucose binding lectin. As this MALDI-IMS workflow has the potential to be applied to any formalin-fixed tissue block or tissue microarray, the advantages and limitations of the technique in context with other glycomic methods are also summarized.

Carbohydrate structure database merged from bacterial, archaeal, plant and fungal parts

The Carbohydrate Structure Databases (CSDBs, http://csdb.glycoscience.ru) store structural, bibliographic, taxonomic, NMR spectroscopic, and other data on natural carbohydrates and their derivatives published in the scientific literature. The CSDB project was launched in 2005 for bacterial saccharides (as BCSDB). Currently, it includes two parts, the Bacterial CSDB and the Plant&Fungal CSDB. In March 2015, these databases were merged to the single CSDB. The combined CSDB includes information on bacterial and archaeal glycans and derivatives (the coverage is close to complete), as well as on plant and fungal glycans and glycoconjugates (almost all structures published up to 1998). CSDB is regularly updated via manual expert annotation of original publications. Both newly annotated data and data imported from other databases are manually curated. The CSDB data are exportable in a number of modern formats, such as GlycoRDF. CSDB provides additional services for simulation of (1)H, (13)C and 2D NMR spectra of saccharides, NMR-based structure prediction, glycan-based taxon clustering and other.