Glycosylation is the most abundant and diverse posttranslational modification of proteins. While several types of glycosylation can be predicted by the protein sequence context, and substantial knowledge of these glycoproteomes is available, our knowledge of the GalNAc-type O-glycosylation is highly limited. This type of glycosylation is unique in being regulated by 20 polypeptide GalNActransferases attaching the initiating GalNAc monosaccharides to Ser and Thr (and likely some Tyr) residues. We have developed a genetic engineering approach using human cell lines to simplify O-glycosylation (SimpleCells) that enables proteome-wide discovery of O-glycan sites using 'bottom-up' ETD-based mass spectrometric analysis. We implemented this on 12 human cell lines from different organs, and present a first map of the human O-glycoproteome with almost 3000 glycosites in over 600 O-glycoproteins as well as an improved NetOGlyc4.0 model for prediction of O-glycosylation. The finding of unique subsets of O-glycoproteins in each cell line provides evidence that the O-glycoproteome is differentially regulated and dynamic. The greatly expanded view of the O-glycoproteome should facilitate the exploration of how site-specific O-glycosylation regulates protein function.

Zinc-finger nuclease (ZFN) gene targeting is emerging as a versatile tool for engineering of multiallelic gene deficiencies. A longstanding obstacle for detailed analysis of glycoproteomes has been the extensive heterogeneities in glycan structures and attachment sites. Here we applied ZFN targeting to truncate the O-glycan elongation pathway in human cells, generating stable 'SimpleCell' lines with homogenous O-glycosylation. Three SimpleCell lines expressing only truncated GalNAcα or NeuAcα2-6GalNAcα O-glycans were produced, allowing straightforward isolation and sequencing of GalNAc O-glycopeptides from total cell lysates using lectin chromatography and nanoflow liquid chromatography-mass spectrometry (nLC-MS/MS) with electron transfer dissociation fragmentation. We identified >100 O-glycoproteins with >350 O-glycan sites (the great majority previously unidentified), including a GalNAc O-glycan linkage to a tyrosine residue. The SimpleCell method should facilitate analyses of important functions of protein glycosylation. The strategy is also applicable to other O-glycoproteomes.

Mucin-type O-glycosylation is initiated by UDP-Nacetylgalactosamine:polypeptide N-acetylgalactosaminyltransferases (GalNAc-transferases). The role each GalNAc-transferase plays in O-glycosylation is unclear.In this report we characterized the specificity and kinetic properties of three purified recombinant GalNActransferases. GalNAc-T1, -T2, and -T3 were expressed as soluble proteins in insect cells and purified to near homogeneity. The enzymes have distinct but partly overlapping specificities with short peptide acceptor substrates. Peptides specifically utilized by GalNAc-T2 or -T3, or preferentially by GalNAc-T1 were identified. GalNAc-T1 and -T3 showed strict donor substrate specificities for UDP-GalNAc, whereas GalNAc-T2 also utilized UDP-Gal with one peptide acceptor substrate. Glycosylation of peptides based on MUC1 tandem repeat showed that three of five potential sites in the tandem repeat were glycosylated by all three enzymes when one or five repeat peptides were analyzed. However, analysis of enzyme kinetics by capillary electrophoresis and mass spectrometry demonstrated that the three enzymes react at different rates with individual sites in the MUC1 repeat. The results demonstrate that individual GalNActransferases have distinct activities and the initiation of O-glycosylation in a cell is regulated by a repertoire of GalNAc-transferases.To date three human UDP-N-Acetylgalactosamine:polypeptide N-acetylgalactosaminyltransferases (1-3) (GalNAc-transferases) 1 have been identified and characterized (1-4). Although the three GalNAc-transferases show similarities in primary structure with regard to predicted domain structures, sequence motifs, and conserved cysteine residues, the overall amino acid sequence similarity of only 45% suggests that the members of the GalNAc-transferase family have undergone significant changes during evolution. The genes encoding these enzymes are located on different chromosomes and have distinct structures, although some intron positions are conserved, suggesting an evolutionary relationship. 2 The genes are differentially expressed in organs as revealed by Northern analysis (1-3); in particular GalNAc-T3 exhibited a restricted expression pattern. One question addressed here is whether these three GalNAc-transferases are isoenzymes with redundant or unique functions.Hennet et al. (5) recently addressed this question by analyzing mice rendered deficient in a close homologue of GalNAc-T1 by gene targeting. No obvious phenotypic differences were observed and preliminary characterization of the residual GalNAc-transferase activity with a few substrates did not reveal differences in enzyme activities. There was a reduction in GalNAc-transferase activity in ES cells in which the gene was inactivated. It is difficult to assess the full significance of these findings because the enzyme deleted in these studies is not well characterized with respect to substrate specificity and tissue expression pattern. Disruption of Dol-P-Man:polypeptide mannosyltransferases which initiate O-gly...

Aberrant expression of immature truncated O-glycans is a characteristic feature observed on virtually all epithelial cancer cells, and a very high frequency is observed in early epithelial premalignant lesions that precede the development of adenocarcinomas. Expression of the truncated O-glycan structures Tn and sialyl-Tn is strongly associated with poor prognosis and overall low survival. The genetic and biosynthetic mechanisms leading to accumulation of truncated O-glycans are not fully understood and include mutation or dysregulation of glycosyltransferases involved in elongation of O-glycans, as well as relocation of glycosyltransferases controlling initiation of O-glycosylation from Golgi to endoplasmic reticulum. Truncated O-glycans have been proposed to play functional roles for cancer-cell invasiveness, but our understanding of the biological functions of aberrant glycosylation in cancer is still highly limited. Here, we used exome sequencing of most glycosyltransferases in a large series of primary and metastatic pancreatic cancers to rule out somatic mutations as a cause of expression of truncated O-glycans. Instead, we found hypermethylation of core 1 β3-Gal-T-specific molecular chaperone, a key chaperone for O-glycan elongation, as the most prevalent cause. We next used gene editing to produce isogenic cell systems with and without homogenous truncated O-glycans that enabled, to our knowledge, the first polyomic and side-by-side evaluation of the cancer O-glycophenotype in an organotypic tissue model and in xenografts. The results strongly suggest that truncation of O-glycans directly induces oncogenic features of cell growth and invasion. The study provides support for targeting cancer-specific truncated O-glycans with immunotherapeutic measures.epigenetics | glycans | skin | pancreas | keratinocyte

Chilling rapidly (<4 h) clusters Glycoprotein - (GP)Ib receptors on blood platelets, and ß2-integrins of hepatic macrophages bind ßGlcNAc residues in the clusters leading to rapid clearance of acutely chilled platelets following transfusion. Although capping the ßGlcNAc moieties by galactosylation prevents clearance, this strategy is ineffective after prolonged (>24 h) refrigeration. We report here that prolonged refrigeration increases the density/concentration of exposed galactose residues such that hepatocytes become increasingly involved in the removal of platelets using their Ashwell-Morell receptors. Macrophages always rapidly remove a large fraction of transfused platelets (~40%). With platelet cooling, hepatocyte-dependent clearance further diminishes their recoveries following transfusion.

Auto-antibodies to cancer antigens hold great promise as sensitive amplified biomarkers for early detection of cancer. Most high through-put strategies to discover such auto-antibodies largely fail to allow identification of antibodies specific for cancer-associated posttranslational modified variants of normal proteins. We hypothesized that aberrant processed proteins are likely auto-antibody targets. MUC1 is over-expressed and aberrantly glycosylated in many cancers and we sought to evaluate the potential of natural cancer-induced auto-antibodies to such aberrant O-glycoforms of MUC1 as sensitive diagnostic biomarkers of disease. We first demonstrated, using an antibody-based glycoprofiling ELISA, that circulating mucins in cancer patients exclude truncated aberrant cancer-associated glycoforms. We then developed an O-glycopeptide microarray and used this to demonstrate detection of IgG antibodies to MUC1 aberrant O-glycopeptide epitopes in patients vaccinated with 25Tn-MUC1-106-mer conjugated to KLH. Finally, screening of sera from breast, ovarian and prostate cancer patients led to identification of three distinct aberrant MUC1 O-glycopeptide epitopes that are targeted by cancer-associated IgG auto-antibodies. The results suggest that auto-antibodies to aberrant O-glycopeptide epitopes may represent a fruitful and previously unaddressed source of sensitive biomarkers for early detection of cancer. The methods developed for chemoenzymatic synthesis of O-glycopeptides in combination with microarrays allow for broader data-mining of the entire cancer O-glycopeptidome.

Enveloped viruses encompass some of the most common human pathogens causing infections of different severity, ranging from no or very few symptoms to lethal disease as seen with the viral hemorrhagic fevers. All enveloped viruses possess an envelope membrane derived from the host cell, modified with often heavily glycosylated virally encoded glycoproteins important for infectivity, viral particle formation and immune evasion. While N-linked glycosylation of viral envelope proteins is well characterized with respect to location, structure and site occupancy, information on mucin-type O-glycosylation of these proteins is less comprehensive. Studies on viral glycosylation are often limited to analysis of recombinant proteins that in most cases are produced in cell lines with a glycosylation capacity different from the capacity of the host cells. The glycosylation pattern of the produced recombinant glycoproteins might therefore be different from the pattern on native viral proteins. In this review, we provide a historical perspective on analysis of viral glycosylation, and summarize known roles of glycans in the biology of enveloped human viruses. In addition, we describe how to overcome the analytical limitations by using a global approach based on mass spectrometry to identify viral O-glycosylation in virus-infected cell lysates using the complex enveloped virus herpes simplex virus type 1 as a model. We underscore that glycans often pay important contributions to overall protein structure, function and immune recognition, and that glycans represent a crucial determinant for vaccine design. High throughput analysis of glycosylation on relevant glycoprotein formulations, as well as data compilation and sharing is therefore important to identify consensus glycosylation patterns for translational applications.

Production of glycoprotein therapeutics in Chinese hamster ovary (CHO) cells is limited by the cells' generic capacity for N-glycosylation, and production of glycoproteins with desirable homogeneous glycoforms remains a challenge. We conducted a comprehensive knockout screen of glycosyltransferase genes controlling N-glycosylation in CHO cells and constructed a design matrix that facilitates the generation of desired glycosylation, such as human-like α2,6-linked sialic acid capping. This engineering approach will aid the production of glycoproteins with improved properties and therapeutic potential.