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Grant
Agency: European Commission | Branch: FP7 | Program: MC-ITN | Phase: FP7-PEOPLE-2013-ITN | Award Amount: 3.45M | Year: 2013

Protozoan parasites and helminths are the cause of some of the most devastating diseases worldwide and a major effort is needed to be able to control or eliminate these diseases. Glycoconjugates are abundant and ubiquitous on the surface of many parasites and they are frequently involved in their survival strategies by forming a protective barrier against host defences. A common feature of the parasites cell surface architecture is the presence of an elaborate and often highly decorated glycocalyx that allows it to interact and respond to the external environment. Therefore, the study of the glycobiology of these organisms offers unique opportunities to devise novel strategies to tackle parasitic-caused diseases. However, the exquisite diversity of these glycoconjugates and of their biosynthetic machineries, the difficulties related with their structural analysis and the complexity associated with their synthesis in the laboratory, poses a tremendous challenge for the scientific community. To address these challenges GlycoPar proposes to establish a European based training programme in a world-class collaborative research environment steered by some of the world leaders in the fast evolving field of parasite glycobiology, in close association with European industrial enterprises. The researchers recruited through this initiative will be exposed, both at the local and network-wide level, to a multicultural and highly multidisciplinary PhD training. This programme will acquaint them with a complete range of state-of-the-art glycobiology methodologies, alongside with valuable transferable and entrepreneurial skills. All together the aim is to create a PhD-level trained generation of young scientists capable of tackling the challenges that parasite glycobiology implies with improved career prospects and employability as well as preparing them to become future leaders in research institutions and industry.


Grant
Agency: European Commission | Branch: FP7 | Program: CP-FP | Phase: HEALTH.2011.1.1-1 | Award Amount: 7.80M | Year: 2011

Glycosylation is a post-translational modification that enriches protein complexity and function. Dysregulation of glycosylation is associated with a wide range of diseases, including cancer, diabetes, as well as congenital, cardiovascular, immunological and infectious disorders. A number of studies identified potentially important glycan disease biomarkers. With regard to biotechnology, proper glycosylation of biologicals is important, as deviations in glycosylation are known to be associated with adverse drug reactions and reduced therapeutic efficacy. However, glycomics is significantly lagging behind genomics and proteomics, mainly due to the absence of high-throughput analytical methods which can reliably quantify a multitude of glycan structures in complex biological samples. We are confident that by coordinated efforts of leading European scientists in glycan analysis using HPLC, MS and CGE-LIF technologies this project will make a decisive step forward by developing real high-throughput tools for glycosylation analysis. By teaming up with leading European researchers in the field of genome wide association studies this project will perform validation of all methods on extremely well characterized set of samples resulting from the FP6 EuroSpan project. The addition of the newly generated glycome data to the pre-existing information about these individuals will enable development of methods for the systems biology approach analysis of the glycome which will integrate glycomic, genomic and environmental data about thousands of individuals. The same methods will also be adapted for quality control and monitoring in the production of biopharmaceuticals. Strong participation of SMEs in the project and close contacts with large industrial partners will ensure that research accomplishments achieved by collaboration between academic and industrial scientists are swiftly transformed into innovative products and services for the benefit of European industry.


Grant
Agency: European Commission | Branch: FP7 | Program: MC-ITN | Phase: PEOPLE-2007-1-1-ITN | Award Amount: 4.07M | Year: 2008

The development and production of glycoarrays will provide the foreground knowledge necessary to lead to a step change in the diagnosis and treatment of diseases ranging from cancers to autoimmune diseases. Carbohydrates play a pivotal role in the molecular interactions that govern biological events at the centre of health and disease. This has become more evident as the characterisation and identification of proteins and their interactions through proteomics has advanced during the last decade. Whilst proteomics is providing a wealth of information, it does not deal with the results of post-translational modifications such as glycosylation which are frequently the driving force behind the biological activity of proteins. This lack of information is beginning to be addressed by the emerging field of glycomics, the mapping of all carbohydrate-protein interactions. The proposed training network is multidisciplinary involving carbohydrate chemistry, array technology and application. The programme offers young scientist an outstanding opportunity to be involved in the development stages of the glycoarray technology and apply this technology to important biological questions.


Grant
Agency: European Commission | Branch: FP7 | Program: CP-FP | Phase: HEALTH.2012.2.4.5-2 | Award Amount: 8.55M | Year: 2012

Inflammatory bowel diseases affect 0.8% of the Europeans, and are associated with high morbidity, definite mortality and an increasing economic burden. Current diagnostic tools and therapeutics for IBD are unsatisfactory. Development of biomarkers allowing insights into pathogenesis, prognosis and targeted therapy is a major unmet need. This programme addresses that need. IBD-BIOM is a multidisciplinary consortium of leading academic and industrial SME researchers in inflammatory bowel disease, genomics, glycomics, glycoproteomics and activomics. Recent genome-wide association studies performed by IBD-BIOM partners have identified nearly 100 genes associated with IBD, but clinical application of these is so far limited. IBD-BIOM will capitalise on its existing high quality clinical, genetic, biochemical and immunological data and biological samples on over 6000 very well characterised IBD patients and controls by exploiting novel technological approaches made available through the expertise and global leading position of IBD-BIOM partners. These comprise cutting edge epigenetic, glycomic, glycoproteomic and activomic approaches which were all previously reported to be associated with inflammation and disturbances to the immune system. The inclusion of these complementary analyses in the diagnostics of IBD should also facilitate elucidation of pathways through which environmental exposures influence IBD risk and progression. A complex systems biology approach will be used to integrate, interrogate and understand this multidimensional dataset to identify novel early diagnostic and prognostic biomarkers and new targets for therapeutic intervention. The track record of achievement of IBD-BIOM partners coupled to the central and leading positions of the research-intensive SME partners in IBD-BIOM is a strong indication that the ambitions work programme will be achieved and a framework to facilitate swift conversion of research discoveries into commercial products.


Grant
Agency: European Commission | Branch: H2020 | Program: MSCA-ITN-ETN | Phase: MSCA-ITN-2015-ETN | Award Amount: 3.29M | Year: 2015

Colorectal cancer (CRC) is a major worldwide cancer burden with about 1.4 million cases in 2012 and an annual mortality of approximately 700,000. Early detection is crucial as treatment is most efficient in early stages where population based screenings could substantially reduce incidence and mortality. Current screening techniques are invasive or lack sensitivity and specificity. Moreover, the molecular mechanisms leading to the formation of different antigens suggested as CRC biomarkers and potential therapeutic targets are poorly understood, especially with regard to carbohydrate-based molecules, such as glycans. Enhancing our understanding of the structure-function relationship of glycosylation in CRC could lead to the discovery of improved diagnostic and prognostic biomarkers and pave the way for nov-el therapeutic targets. Building on an established network of analysts with many years of experience in (glyco)proteomics and biomarker research, in collaboration with colleagues in the field of glycobiology and glyco-immunology, GlyCoCan will develop new methods, and use current state of the art methods, to investigate the role of glycosylation in many different aspects of CRC. The GlyCoCan multi-disciplinary network will principally be a training programme with a substantial industrial focus on technology transfer and teaching of internationally adopted biopharma regulations (GMP, ISO9001, ICH guidelines). The underlying specific research objectives will be addressed within individual ESR projects, giving rise to a generation of ESRs whose main focus is investigating and tackling the challenges of the role of glycosylation within CRC and other diseases. The network will address the currently unmet need for glycosylation researchers with an inter-disciplinary perspective to fully exploit the immense potential of the young scientific field of glyco-oncology and to set them on a path to successful and productive careers in academic and industrial collaborations.


Grant
Agency: European Commission | Branch: H2020 | Program: MSCA-ITN-EID | Phase: MSCA-ITN-2016 | Award Amount: 1.55M | Year: 2016

GlySign is a research training network for the translation of glycomic clinical biomarkers for Precision Medicine (PM). Complex, distinctive changes occur in the glycomics profiles or - Glycan Signatures - of human glycoproteins during progression of many chronic diseases including cancer and inflammatory conditions. The three beneficiaries of the GlySign Consortium have been instrumental in contributing to knowledge in this field through development of glycomics technology and discovery of clinically important novel glycan biomarkers in a variety of diseases. Glycan signatures have great potential for adding useful diagnostic and prognostic information in PM. However, advancement of this field is slow because (a) glycans have immense structural complexity resulting in major technical challenges for their analysis and (b) there is a lack of experts with required glycoanalytical skills. GlySign will address this gap by training six young scientists within an innovative training-by-research programme with high industrial-academic mobility to eventually push forward the translation of novel glycomics-based diagnostic tools into clinical practice. This will be achieved by further developing a range of selective and sensitive glycomics technologies for the analysis of samples from patients and healthy controls in close collaboration between industry/academia as well as clinical chemists and clinicians who will be the end users of GlySigns final products. To this end, we will focus the training on clinical glycomics applied to four model diseases implicating changes in the glycosylation of circulating proteins specific to disease progression or subtype, i.e. diabetes, prostate cancer, fetal and neonatal alloimmune thrombocytopenia and rheumatoid arthritis. Due to its strong industrial and translational focus, GlySign will, moreover, fill a current gap in the market by establishing new in vitro diagnostic platforms for clinical exploitation of glycomic biomarkers for PM.


Domann P.,LGC Ltd. Middlesex | Spencer D.I.R.,Ludger Ltd. | Harvey D.J.,University of Oxford
Rapid Communications in Mass Spectrometry | Year: 2012

Although negative ion fragmentation mass spectra of neutral N-linked carbohydrates (those attached to Asn in glycoproteins) provide much more structural information than spectra recorded in positive ion mode, neutral carbohydrates are reluctant to form negative ions by matrix-assisted laser desorption/ionization (MALDI) unless ionized from specific matrices such as nor-harmane or adducted with anions such as chloride. This paper reports the results of experiments to optimize negative ion formation from adducts of N-linked glycans with respect to ion abundance and fragment ion production. The best results were obtained with 2,4,6-trihydroxyacetophenone (THAP) as the matrix with added ammonium nitrate as the salt providing the anion. This approach is demonstrated to be applicable for a wide range of N-linked glycan structures. Phosphate adducts, analogous to those that are usually encountered in electrospray spectra from N-glycans released by protein N-glycosidase F, were produced by addition of ammonium phosphate to the matrix but in relatively low yield allowing competitive ionization of endogenous anionic compounds leading to complex spectra. Fragmentation of the nitrate adducts, which were formed in higher yield, generally paralleled that seen by collision-induced dissociation following ionization by electrospray, with the first stage of the dissociation being the elimination of the nitrate with a proton from one of the hydroxyl groups of the sugar. The spectra of the resulting [M-H]- species displayed very specific fragment ions, mainly cross-ring and C-type glycosidic cleavage products, that revealed more structural (linkage and branching) information of the compounds than the mainly glycosidic cleavage products that dominated the positive ion spectra. Copyright © 2012 John Wiley & Sons, Ltd.


Zauner G.,Leiden University | Kozak R.P.,Ludger Ltd. | Gardner R.A.,Ludger Ltd. | Fernandes D.L.,Ludger Ltd. | And 2 more authors.
Biological Chemistry | Year: 2012

This review provides an overview on the methods available for analysis of O-glycosylation. Three major themes are addressed: analysis of released O-glycans including different O-glycan liberation, derivatization, and detection methods; analysis of formerly O-glycosylated peptides yielding information on O-glycan attachment sites; analysis of O-glycopeptides, representing by far the most informative but also most challenging approach for O-glycan analysis. Although there are various techniques available for the identification of O-linked oligosaccharides, the focus here is on MS fragmentation techniques such as collision-induced fragmentation, electron capture dissociation, and electron transfer dissociation. Finally, the O-glycan analytical challenges that need to be met will be discussed. Copyright © by Walter de Gruyter • Berlin • Boston.


Kozak R.P.,Ludger Ltd. | Royle L.,Ludger Ltd. | Gardner R.A.,Ludger Ltd. | Fernandes D.L.,Ludger Ltd. | Wuhrer M.,Leiden University
Analytical Biochemistry | Year: 2012

The analysis of O-glycans is essential for better understanding their functions in biological processes. Although many techniques for O-glycan release have been developed, the hydrazinolysis release method is the best for producing O-glycans with free reducing termini in high yield. This release technique allows the glycans to be labeled with a fluorophore and analyzed by fluorescence detection. Under the hydrazinolysis release conditions, a side reaction is observed and causes the loss of monosaccharides from the reducing terminus of the glycans (known as peeling). Using bovine fetuin (because it contains the sialylated O-glycans most commonly found on biopharmaceuticals) and bovine submaxillary gland mucin (BSM), here we demonstrate that peeling can be greatly reduced when the sample is buffer exchanged prior to hydrazinolysis with solutions of either 0.1% trifluoroacetic acid (TFA) or low-molarity (100, 50, 20, and 5 mM) ethylenediaminetetraacetic acid (EDTA). The addition of calcium chloride to fetuin resulted in an increase in peeling, whereas subsequent washing with EDTA abolished this effect, suggesting a role of calcium and possibly other cations in causing peeling. The presented technique for sample preparation prior to hydrazinolysis greatly reduces the level of undesirable cleavage products in O-glycan analysis and increases the robustness of the method. © 2012 Elsevier Inc. All rights reserved.

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