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• Conference paper
  Liu Y, Catera R, Gao C, Yan J, Magli A, Allen SL, Rai K, Chu CC, Stamatopoulos K, Chiorazzi N, Kolitz JE, Feizi Tet al., 2017,

  The (auto)antigen specificities of B cell receptor immunoglobulins from CLL stereotyped subset 4 are positively and negatively selected by structural elements introduced by somatic mutation and isotype class switching

  , Publisher: TAYLOR & FRANCIS LTD, Pages: 80-81, ISSN: 1042-8194
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• Conference paper
  Akune Y, Arpinar S, Stoll M, Silva LM, Palma AS, Liu Y, Ranzinger R, Feizi Tet al., 2017,

  New software for glycan array for data processing, storage and presentation

  , Annual Meeting of the Society-for-Glycobiology, Publisher: OXFORD UNIV PRESS INC, Pages: 1204-1204, ISSN: 0959-6658
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• Journal article
  Li Z, Gao C, Zhang Y, Palma A, Childs R, Silva L, Liu Y, Jiang X, Liu Y, Chai W, Feizi Tet al., 2017,

  O-Glycome beam search arrays for carbohydrate ligand discovery

  , Molecular and Cellular Proteomics, Vol: 17, Pages: 121-133, ISSN: 1535-9476

  O-glycosylation is a post-translational modification of proteins crucial to molecular mechanisms in health and disease. O-glycans are typically highly heterogeneous. The involvement of specific O-glycan sequences in many bio-recognition systems is yet to be determined due to a lack of efficient methodologies. We describe here a targeted microarray approach: O-glycome beam search that is both robust and efficient for O-glycan ligand-discovery. Substantial simplification of the complex O-glycome profile and facile chromatographic resolution is achieved by arraying O-glycans as branches, monitoring by mass spectrometry, focusing on promising fractions, and on-array immuno-sequencing. This is orders of magnitude more sensitive than traditional methods. We have applied beam search approach to porcine stomach mucin and identified extremely minor components previously undetected within the O-glycome of this mucin that are ligands for the adhesive proteins of two rotaviruses. The approach is applicable to O-glycome recognition studies in a wide range of biological settings to give insights into glycan recognition structures in natural microenvironments.

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• Conference paper
  Panagos C, Moss C, Bavington C, Mulloy B, Feizi T, Chai W, Woods R, Uhrin Det al., 2017,

  Analysis of the 3D structure of fucosylated chondroitin sulfate from H. forskali and its interaction with selectins

  , 254th National Meeting and Exposition of the American-Chemical-Society (ACS) on Chemistry's Impact on the Global Economy, Publisher: AMER CHEMICAL SOC, ISSN: 0065-7727
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• Journal article
  Catera R, Liu Y, Gao C, Yan X-J, Magli A, Allen SL, Kolitz JE, Rai KR, Chu CC, Feizi T, Stamatopoulos K, Chiorazzi Net al., 2017,

  Binding of CLL Subset 4 B Cell Receptor Immunoglobulins to Viable Human Memory B Lymphocytes Requires a Distinctive IGKV Somatic Mutation

  , MOLECULAR MEDICINE, Vol: 23, Pages: 1-12, ISSN: 1076-1551
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  • Citations: 8
• Journal article
  Liu Y, McBride R, Stoll M, Palma AS, Silva L, Agravat S, Aoki-Kinoshita KF, Campbell MP, Costello CE, Dell A, Haslam SM, Karlsson NG, Khoo K-H, Kolarich D, Novotny M, Packer NH, Ranzinger R, Rapp E, Rudd PM, Struwe WB, Tiemeyer M, Wells L, York WS, Zaia J, Kettner C, Paulson JC, Feizi T, Smith DFet al., 2016,

  The Minimum Information Required for a Glycomics Experiment (MIRAGE) project: improving the standards for reporting glycan microarray-based data

  , Glycobiology, Vol: 27, Pages: 280-284, ISSN: 1460-2423

  MIRAGE (Minimum Information Required for A Glycomics Experiment) is an initiative that was created by experts in the fields of glycobiology, glycoanalytics, and glycoinformatics to produce guidelines for reporting results from the diverse types of experiments and analyses used in structural and functional studies of glycans in the scientific literature. As a sequel to the guidelines for sample preparation (Struwe et al. 2016, Glycobiology, 26, 907-910) and mass spectrometry (MS) data (Kolarich et al. 2013, Mol. Cell Proteomics. 12, 991-995), here we present the first version of guidelines intended to improve the standards for reporting data from glycan microarray analyses. For each of eight areas in the workflow of a glycan microarray experiment, we provide guidelines for the minimal information that should be provided in reporting results. We hope that the MIRAGE glycan microarray guidelines proposed here will gain broad acceptance by the community, and will facilitate interpretation and reproducibility of the glycan microarray results with implications in comparison of data from different laboratories and eventual deposition of glycan microarray data in international databases.

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• Conference paper
  Correia VG, Bras JLA, Liu Y, Silva L, Zhang Y, Pinheiro BA, Romao MJ, Carvalho AL, Chai W, Fontes CMGA, Feizi T, Palma ASet al., 2016,

  An integrative strategy to decipher glycan recognition in the human gut microbiome

  , Annual Meeting of the Society-for-Glycobiology, Publisher: OXFORD UNIV PRESS INC, Pages: 1398-1399, ISSN: 0959-6658
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• Journal article
  Bartels MF, Winterhalter PR, Yu J, Liu Y, Lommel M, Möhrlen F, Hu H, Feizi T, Westerlind U, Ruppert T, Strahl Set al., 2016,

  Protein O-Mannosylation in the Murine Brain: Occurrence of Mono-O-Mannosyl Glycans and Identification of New Substrates

  , PLOS One, Vol: 11, ISSN: 1932-6203

  Protein O-mannosylation is a post-translational modification essential for correct development of mammals. In humans, deficient O-mannosylation results in severe congenital muscular dystrophies often associated with impaired brain and eye development. Although various O-mannosylated proteins have been identified in the recent years, the distribution of O-mannosyl glycans in the mammalian brain and target proteins are still not well defined. In the present study, rabbit monoclonal antibodies directed against the O-mannosylated peptide YAT(α1-Man)AV were generated. Detailed characterization of clone RKU-1-3-5 revealed that this monoclonal antibody recognizes O-linked mannose also in different peptide and protein contexts. Using this tool, we observed that mono-O-mannosyl glycans occur ubiquitously throughout the murine brain but are especially enriched at inhibitory GABAergic neurons and at the perineural nets. Using a mass spectrometry-based approach, we further identified glycoproteins from the murine brain that bear single O-mannose residues. Among the candidates identified are members of the cadherin and plexin superfamilies and the perineural net protein neurocan. In addition, we identified neurexin 3, a cell adhesion protein involved in synaptic plasticity, and inter-alpha-trypsin inhibitor 5, a protease inhibitor important in stabilizing the extracellular matrix, as new O-mannosylated glycoproteins.

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• Journal article
  Zhang H, Palma AS, Zhang Y, Childs RA, Liu Y, Mitchell DA, Guidolin LS, Weigel W, Mulloy B, Ciocchini AE, Feizi T, Chai Wet al., 2016,

  Generation and characterization of β1,2-gluco-oligosaccharide probes from Brucella abortus cyclic β-glucan and their recognition by C-type lectins of the immune system

  , Glycobiology, Vol: 26, Pages: 1086-1096, ISSN: 1460-2423

  The β1,2-glucans produced by bacteria are important in invasion, survival andimmunomodulation in infected hosts be they mammals or plants. However, there has been alack of information on proteins which recognize these molecules. This is partly due to theextremely limited availability of the sequence-defined oligosaccharides and derived probesfor use in the study of their interactions. Here we have used the cyclic β1,2-glucan (CβG) ofthe bacterial pathogen Brucella abortus, after removal of succinyl side chains, to preparelinearized oligosaccharides which were used to generate microarrays. We describe optimizedconditions for partial depolymerization of the cyclic glucan by acid hydrolysis and conversionof the β1,2-gluco-oligosaccharides, with degrees of polymerization 2-13, to neoglycolipids forthe purpose of generating microarrays. By microarray analyses we show that the C-type lectinreceptor DC-SIGNR, like the closely related DC-SIGN we investigated earlier, binds to theβ1,2-gluco-oligosaccharides, as does the soluble immune effector serum mannose-bindingprotein. Exploratory studies with DC-SIGN are suggestive of the recognition also of the intactCβG by this receptor. These findings open the way to unravelling mechanisms ofimmunomodulation mediated by β1,2-glucans in mammalian systems.

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• Journal article
  Liu Y, Ramelot TA, Huang P, Liu Y, Li Z, Feizi T, Zhong W, Wu FT, Tan M, Kennedy MA, Jiang Xet al., 2016,

  Glycan specificity of P[19] rotavirus and comparison with those of other related P genotypes

  , Journal of Virology, Vol: 90, Pages: 9983-9996, ISSN: 1098-5514

  The P[19] genotype belongs to the P[II] genogroup of group A rotaviruses (RVs). However, unlike the other P[II] RVs that mainly infects humans, P[19] RVs commonly infect animals (porcine), making P[19] unique to study RV diversity and host ranges. Through in vitro binding assays and saturation transfer difference (STD) NMR, we found that P[19] could bind mucin cores 2, 4, and 6, as well as type 1 histo-blood group antigens (HBGAs). The common sequences of these glycans serve as minimal binding units, while additional residues, such as the A, B, H, and Lewis epitopes of the type 1 HBGAs, can further define the binding outcomes and therefore, likely the host ranges for P[19] RVs. This complex binding property of P[19] is shared with those of the other three P[II] RVs (P[4], P[6] and P[8]) in that all of them recognized the type 1 HBGA precursor, although P[4] and P[8], but not P[6], also bind to mucin cores. Moreover, while essential for P[4] and P[8] binding, the addition of the Lewis epitope blocked P[6] and P[19] binding to type 1 HBGAs. Chemical shift NMR of P[19] VP8* identified a ligand binding interface that has shifted away from the known RV P-genotype binding sites but is conserved among all P[II] RVs and two P[I] RVs (P[10] and P[12]), suggesting an evolutionary connection among these human and animal RVs. Taken together, these data are important for hypotheses on potential mechanisms for RV diversity, host ranges, and cross-species transmission. IMPORTANCE: In this study, we found that this P[19] strain and other P[II] RVs recognize mucin cores and the type 1 HBGA precursors as the minimal functional units and that additional saccharides adjacent to these units can alter binding outcomes and thereby possibly host ranges. These data may help to explain why some P[II] RVs, such as P[6] and P[19], commonly infect animals but rarely humans, while others, such as the P[4] and P[8] RVs, mainly infect humans and are predominant over other P genotypes. Elucidation

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