The minimum information required for a glycomics experiment (MIRAGE) project: improving the standards for reporting glycan microarray-based data

Liu, Yan; McBride, Ryan; Stoll, Mark S.; Palma, Angelina S.; Silva, Lisete M.; Agravat, Sanjay; Aoki‐Kinoshita, Kiyoko F.; Campbell, Matthew P.; Costello, Catherine E.; Dell, Anne; Haslam, Stuart M.; Karlsson, Niclas G.; Khoo, Kay‐Hooi; Kolarich, Daniel; Novotný, Miloš V.; Packer, Nicolle H.; Ranzinger, René; Rapp, Erdmann; Rudd, Pauline M.; Struwe, Weston B.; Tiemeyer, Michael; Wells, Lance; York, William S.; Zaia, Joseph; Kettner, Carsten; Paulson, James C.; Feizi, Ten; Smith, David F.

doi:10.1093/glycob/cww118

Cited by 73 publications

(60 citation statements)

References 35 publications

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“…This limitation has obvious consequences for ligand discovery [45 •• ], and for the elucidation of structure-specificity relationships. Although at present, data from glycan array screening need generally to be treated qualitatively, community-wide standards are being developed [117], which together with more quantitative approaches to data processing [64 •• ] and computational analysis [118 • ,119 • ], will enhance the interpretability of such data. A powerful example of the generation and use of quantitative surface K D values from glycan array screening was reported by Wong et al [120 •• ].…”

Section: Discussionmentioning

confidence: 99%

New insights into influenza A specificity: an evolution of paradigms

White

Hadden

et al. 2017

Current Opinion in Structural Biology

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Understanding the molecular origin of influenza receptor specificity is complicated by the paucity of quantitative affinity measurements, and the qualitative and variable nature of glycan array data. Further obstacles arise from the varied impact of viral glycosylation and the relatively narrow spectrum of biologically relevant receptors present on glycan arrays. A survey of receptor conformational properties is presented, leading to the conclusion that conformational entropy plays a key role in defining specificity, as does the newly reported ability of biantennary receptors that terminate in Siaα2-6Gal sequences to form bidentate interactions to two binding sites in a hemagglutinin trimer. Bidentate binding provides a functional explanation for the observation that Siaα2-6 receptors adopt an open-umbrella topology when bound to hemagglutinins from human-infective viruses, and calls for a reassessment of virus avidity and tissue tropism.

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Section: Discussionmentioning

confidence: 99%

New insights into influenza A specificity: an evolution of paradigms

White

Hadden

et al. 2017

Current Opinion in Structural Biology

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“…All steps were carried out at ambient temperature. Details of the glycan library including the sources of saccharides, the generation of the microarrays, imaging, and data analysis are in the Supplementary glycan microarray document (S Table 4) in accordance with the Minimum Information Required for A Glycomics Experiment (MIRAGE) guidelines for reporting glycan microarray-based data [93].…”

Section: Methodsmentioning

confidence: 99%

Mannan detecting C-type lectin receptor probes recognise immune epitopes with diverse chemical, spatial and phylogenetic heterogeneity in fungal cell walls

Vendele

Willment

Silva

et al. 2019

Preprint

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29During the course of fungal infection, pathogen recognition by the innate immune system is 30 critical to initiate efficient protective immune responses. The primary event that triggers 31 immune responses is the binding of Pattern Recognition Receptors (PRRs), which are 32 expressed at the surface of host immune cells, to Pathogen-Associated Molecular Patterns 33 (PAMPs) located predominantly in the fungal cell wall. Most fungi have mannosylated PAMPs 34 in their cell walls and these are recognized by a range of C-type lectin receptors (CTLs). 35However, the precise spatial distribution of the ligands that induce immune responses within 36 the cell walls of fungi are not well defined. We used recombinant IgG Fc-CTLs fusions of three 37 murine mannan detecting CTLs, including dectin-2, the mannose receptor (MR) carbohydrate 38 recognition domains (CRDs) 4-7 (CRD4-7), and human DC-SIGN (hDC-SIGN) and the β-1,3 39 glucan-binding lectin dectin-1 to map PRR ligands in the fungal cell wall. We show that 40 epitopes of mannan-specific CTL receptors can be clustered or diffuse, superficial or buried 41 in the inner cell wall. We demonstrate that PRR ligands do not correlate well with phylogenetic 42 relationships between fungi, and that Fc-lectin binding discriminated between mannosides 43 expressed on different cell morphologies of the same fungus. We also demonstrate CTL 44 epitope differentiation during different phases of the growth cycle of Candida albicans and that 45 MR and DC-SIGN labelled outer chain N-mannans whilst dectin-2 labelled core N-mannans 46 displayed deeper in the cell wall. These immune receptor maps of fungal walls therefore reveal 47 and capable of changing its composition and organization when adapting to different growth 56 niches and environmental stresses. Differences in the composition of the cell wall lead to 57 differential immune recognition by the host. Understanding how changes in the cell wall 58 composition affect recognition by PRRs is likely to be of major diagnostic and clinical 59 relevance. Here we address this fundamental question using four soluble immune receptor-60 probes which recognize mannans and β-glucan in the cell wall. We use this novel methodology 61 to demonstrate that mannan epitopes are differentially distributed in the inner and outer layers 62 of fungal cell wall in a clustered or diffuse manner. Immune reactivity of fungal cell surfaces 63 did not correlate with relatedness of different fungal species, and mannan-detecting receptor-64 probes discriminated between cell surface mannans generated by the same fungus growing 65 under different conditions. These studies demonstrate that mannan-epitopes on fungal cell 66 surfaces are differentially distributed within and between the cell walls of fungal pathogens. 67 68 receptor-ligand interactions are the primary origin of all immune responses and they promote 82 expression and secretion of various chemokines and cytokines that results in recruitment of 83 neutrophils, macrophages and other immune cell types to the ...

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“…All steps were carried out at ambient temperature. Details of the glycan library including the sources of saccharides, the generation of the microarrays, imaging, and data analysis are in the Supplementary glycan microarray document (S4 Table) in accordance with the Minimum Information Required for A Glycomics Experiment (MIRAGE) guidelines for reporting glycan microarray-based data [93]. experiments ± SEM.…”

Section: Glycan Microarray Analyses Of Fc-lectinsmentioning

confidence: 99%

Mannan detecting C-type lectin receptor probes recognise immune epitopes with diverse chemical, spatial and phylogenetic heterogeneity in fungal cell walls

et al. 2020

Self Cite

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During the course of fungal infection, pathogen recognition by the innate immune system is critical to initiate efficient protective immune responses. The primary event that triggers immune responses is the binding of Pattern Recognition Receptors (PRRs), which are expressed at the surface of host immune cells, to Pathogen-Associated Molecular Patterns (PAMPs) located predominantly in the fungal cell wall. Most fungi have mannosylated PAMPs in their cell walls and these are recognized by a range of C-type lectin receptors (CTLs). However, the precise spatial distribution of the ligands that induce immune responses within the cell walls of fungi are not well defined. We used recombinant IgG Fc-CTLs fusions of three murine mannan detecting CTLs, including dectin-2, the mannose receptor (MR) carbohydrate recognition domains (CRDs) 4-7 (CRD4-7), and human DC-SIGN (hDC-SIGN) and of the β-1,3 glucan-binding lectin dectin-1 to map PRR ligands in the fungal cell wall of fungi grown in vitro in rich and minimal media. We show that epitopes of mannan-specific CTL receptors can be clustered or diffuse, superficial or buried in the inner cell wall. We demonstrate that PRR ligands do not correlate well with phylogenetic relationships between fungi, and that Fc-lectin binding discriminated between mannosides expressed on different cell morphologies of the same fungus. We also demonstrate CTL epitope differentiation during different phases of the growth cycle of Candida albicans and that MR and DC-SIGN labelled outer chain N-mannans whilst dectin-2 labelled core N-mannans displayed deeper in the cell wall. These immune receptor maps of fungal walls of in vitro grown cells therefore reveal remarkable spatial, temporal and chemical diversity, indicating that the triggering of immune recognition events originates from multiple physical origins at the fungal cell surface.

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The minimum information required for a glycomics experiment (MIRAGE) project: improving the standards for reporting glycan microarray-based data

Cited by 73 publications

References 35 publications

New insights into influenza A specificity: an evolution of paradigms

New insights into influenza A specificity: an evolution of paradigms

Mannan detecting C-type lectin receptor probes recognise immune epitopes with diverse chemical, spatial and phylogenetic heterogeneity in fungal cell walls

Mannan detecting C-type lectin receptor probes recognise immune epitopes with diverse chemical, spatial and phylogenetic heterogeneity in fungal cell walls

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