Functional implications of glycans and their curation:insights from the workshop held at the 16th Annual International Biocuration Conference in Padua, Italy

Dynamic changes in protein glycosylation impact human health and disease progression. However, current resources that capture disease and phenotype information focus primarily on the macromolecules within the central dogma of molecular biology (DNA, RNA, proteins). To gain a better understanding of organisms, there is a need to capture the functional impact of glycans and glycosylation on biological processes. A workshop titled "Functional impact of glycans and their curation" was held in conjunction with the 16th Annual International Biocuration Conference to discuss ongoing worldwide activities related to glycan function curation. This workshop brought together subject matter experts, tool developers, and biocurators from over 20 projects and bioinformatics resources. Participants discussed four key topics for each of their resources: (i) how they curate glycan function-related data from publications and other sources, (ii) what type of data they would like to acquire, (iii) what data they currently have, and (iv) what standards they use. Their answers contributed input that provided a comprehensive overview of state-of-the-art glycan function curation and annotations. This report summarizes the outcome of discussions, including potential solutions and areas where curators, data wranglers, and text mining experts can collaborate to address current gaps in glycan and glycosylation annotations, leveraging each other's work to improve their respective resources and encourage impactful data sharing among resources. Database URL: https://wiki.glygen.org/Glycan_Function_Workshop_2023

N-Glycosylation profiles as a risk stratification biomarker for Type II Diabetes Mellitus and its associated factors

Worldwide, the prevalence of cardiometabolic diseases, particularly type II diabetes mellitus (T2DM), and to a lesser extent, metabolic syndrome (MetS), has increased dramatically. Despite this increase, there is still a lack of robust biomarkers for cardiometabolic diseases to secure better clinical outcomes. The enzymatic attachment of oligosaccharides (glycans) to proteins-glycosylation is of metabolic and physiological significance, as exploring aberrations of glycosylation profiles can reveal novel biomarkers. In parallel, this process could also explain the biological mechanisms that underpin a suboptimal health status (SHS), a reversible subclinical stage of a cardiometabolic disease. However, studies on the correlation between glycosylation and MetS/T2DM are scarce and none has thus far been performed on a West African population. Thus, the overall aim of this thesis was to explore complementary biomarker panels of healthy and diseased patients considered relevant to Ghanaian residents. The thesis is structured in the form of five related studies, each addressing a specific aim. From January 2016 to October 2016, a longitudinal case-control study comprising 253 T2DM patients and 260 controls, aged 18-80 years was conducted in Ghana. Fasting plasma samples were collected for clinical assessment, after which plasma N-glycans were analysed by Ultra-Performance Liquid Chromatography (UPLC) and statistical analyses performed. Central adiposity, underweight, high systolic blood pressure (SBP), high diastolic blood pressure (DBP) and high triglycerides (TG) were found to be independent risk factors associated with high SHS after adjusting for age and gender (Study I). SHS score was associated with age, physical inactivity, fasting plasma glucose (FPG), TG and MetS. MetS was associated with increased high branching (HB), trigalactosylated (G3), antennary fucosylated (FUC_A), triantennary (TRIA) and decreased low branching (LB) glycan structures (Study II). The levels of HB, G3, FUC_A, and TRIA N-glycans were increased in T2DM whereas levels of LB, non-sialylated (S0), monogalactosylation (G1), core fucosylation (FUC_C), biantennary galactosylation (A2G) and biantennary (BA) Nglycans were decreased compared to controls (Study III). Biguanides alone, or in combination with sulfonylurea and thiazolidinedione, did not improve glycaemic status at follow-up. Many participants using angiotensin converting enzyme inhibitors achieved desired targets for blood pressure control while statins were effective for control of plasma lipids (Study IV). At a population level, the variability of N-glycan structures ranged from 11% to 56% at both baseline and follow-up, with an average coefficient of variation of 28% and 29%, respectively. The intra-individual N-glycan peak (GP) variations were minor except for GP1 and GP29. However, there were no statistically significant differences in N-glycosylation profiles from baseline to follow-up (Study V). This thesis shows an association between SHS and MetS/T2DM while MetS and T2DM are characterised by increased levels of complex N-glycan structures, and these structures are stable in T2DM over six months. Many of the findings in this thesis agree with earlier studies from Chinese and Croatian populations with major differences attributed to genetic and environmental factors. Future longitudinal studies are required to provide a better understanding of the transition from SHS to T2DM, as well as to validate N-glycans as generic risk stratification biomarkers for a general population

High-throughput mass spectrometric N-glycomics

Glycosylation is an important way in which proteins, the functional agents of our body, can be modified to alter and expand their functional repertoire. Glycans consist of monosaccharides that are linked in a chained and branching fashion, often to form specific epitopes that are of clinical and biopharmaceutical interest. In order to study glycosylation, there is a need for high-throughput analysis methodology. Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) is a prominent example of this, as it can rapidly provide information on the monosaccharide compositions of glycans. However, it is challenging for the method to yield information on the structural aspects of glycosylation, as well as on glycans carrying sialic acids. These sialylated glycans are prone to in-source and metastable decay, and tend to require chemical derivatization to allow their analysis. The aim of this thesis is the development and application of new methodology for MALDI-MS N-glycomics, and, with a focus on metabolic syndrome and rheumatoid arthritis, to increase our understanding of the role of N-glycosylation in health and disease. A principal outcome of the work is a sialic acid derivatization protocol that allows the mass-based discrimination of alpha-2,3- and alpha-2,6-linked sialic acids, facilitating their study in a high-throughput setting. LUMC / Geneeskund

Applications of Glycoconjugates for Enzyme Substrate Specificity Exploration, Immune Therapy, and Carbohydrate-Protein Interaction Study

Locating at the outer surface of cells, glycans and their glycoconjugates play multitude of roles in biological processes. Among these, protein O-GlcNAcylation is involved in a variety of age related diseases, such as Alzheimer’s disease, diabetes, and cancer development. O-GlcNAc cycling is catalyzed by only two enzymes: O-GlcNAc transferase (OGT) and O-GlcNAcase (OGA), raising key questions regarding the regulation and selectivity of these enzymes. In project one, we synthesized a series of glycopeptide substrates with various GlcNAc derivatives to study the specificity of human OGA. Several sugar moieties were discovered to be resistant to OGA hydrolysis which had the potential to be used as O-GlcNAcylation probes through metabolic glycan labeling (MGL). Installation of an antibody-recruiting moiety on the surface of disease-relevant cells can lead to the selective destruction of targets by the immune system. Herein, in project two, taking advantage of MGL strategy, we synthesized the folic acid-azidosugar conjugate and described the development of a new strategy to selectively deliver azidosugar and introduce L-rhamnose antigens via click chemistry onto cancer cell surface. The immune system can be further activated by the installed antigens to clear out cancer cells. Such an approach can be an alternative and potential strategy to traditional chemotherapeutics in cancer therapy and possibly other diseases. Carbohydrate-protein interactions are essential for body function, but implicated to capture and identify. In project three, we aim to develop a novel method to lock carbohydrate-protein interactions in a covalent form. Expanding the genetic code to incorporate crosslinkers into proteins enables us capture and identify unknown glycoproteins, manipulate carbohydrate-protein interactions, and study the glycan-related downstream biological signaling

The computational analysis of post-translational modifications

The post-translational modification (PTMs) of proteins presents a means to increase the proteome size and diversity of an organism through the inclusion of structural elements not encoded at the sequence-level alone. Their erroneous inclusion or exclusion has been linked to a variety of diseases and disorders thus their characterisation has the potential to present viable drug targets. The proliferation of newer high-throughput methods, such as mass spectrometry, to identify such modifications has led to a rapid increase in the number of databases and tools to display and analyse such vast amounts of data effectively. This study covers the development of one such tool; PTM Browser, and the construction of the underlying database that it is based upon. This new database was initially seeded with annotations from the Swiss-Prot and Phospho.ELM resources. The initial database of PTMs was then expanded to include a large repertoire of previously unannotated proteins for a selection of topical species (e.g. Danio rerio and Tetraodon nigroviridis). Orthologue assignments have also been added to the database – to allow for queries to be performed regarding the conservation of modifications between homologous proteins. The PTM Browser tool allows for a full exploration of this new database of PTMs – with a special focus on allowing users to identify modifications that are both shared between and are specific to particular species. This tool is freely available for non-commercial use at the following URL: http://www.ptmbrowser.org. An analysis is presented on the conservation of modifications between members of the tumour suppressor family, p53, using this new tool. This tool has also been used to analysis the conservation of modifications between super-kingdoms and Eukaryote species

Thermophilic microorganisms as source of molecules for biotechnological applications

Background: The spore-forming lactic acid bacterium Bacillus coagulans MA-13 has been isolated from canned beans manufacturing and successfully employed for the sustainable production of lactic acid from lignocellulosic biomass. Among lactic acid bacteria, B. coagulans strains are generally recognized as safe (GRAS) for human consumption. Low-cost microbial production of industrially valuable products such as lactic acid and various enzymes devoted to the hydrolysis of oligosaccharides and lactose is of great importance to the food industry. Specifically, α- and β-galactosidases are attractive for their ability to hydrolyze not-digestible galactosides present in the food matrix as well as in the human gastrointestinal tract. Results: In this thesis, the potential of B. coagulans MA-13 as a source of metabolites and enzymes has been explored to improve the digestibility and the nutritional value of food. A combination of mass spectrometry analysis with conventional biochemical approaches has been employed to unveil the intra- and extra-cellular glycosyl hydrolases (GH) repertoire of B. coagulans MA-13 under diverse growth conditions. The highest enzymatic activity was detected on β-1,4 and α-1,6-glycosidic linkages and the enzymes responsible for these activities were unambiguously identified as a β-galactosidase (GH42) and an α-galactosidase (GH36), respectively. Whilst the former has been found only in the cytosol, the latter is localized also extracellularly. The export of this enzyme may occur through a not yet identified secretion mechanism since a typical signal peptide is missing in the α-galactosidase sequence. A full biochemical characterization of the recombinant β-galactosidase has been carried out and the ability of this enzyme to perform homo- and hetero-condensation reactions to produce galacto-oligosaccharides, has been demonstrated. Conclusions: Probiotics that are safe for human use and are capable of producing high levels of both α-galactosidase and β-galactosidase are of great importance to the food industry. In this thesis, it has been proven the ability of B. coagulans MA-13 to over-produce these two enzymes thus paving the way for its potential use in food industry