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

Glycobiology

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 KH, Kolarich D, Novotny MV, 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 DF.
PMID: 27993942
Glycobiology. 2017 Apr;27(4):280-284. doi: 10.1093/glycob/cww118. Epub 2016 Nov 22.

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...

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Liu Y, McBride R, Stoll M, et al. The minimum information required for a glycomics experiment (MIRAGE) project: improving the standards for reporting glycan microarray-based data. Glycobiology. 2016;27(4):280-284doi: 10.1093/glycob/cww118.
Liu, Y., McBride, R., Stoll, M., Palma, A. S., Silva, L., Agravat, S., Aoki-Kinoshita, K. F., Campbell, M. P., Costello, C. E., Dell, A., Haslam, S. M., Karlsson, N. G., Khoo, K. H., Kolarich, D., Novotny, M. V., Packer, N. H., Ranzinger, R., Rapp, E., Rudd, P. M., Struwe, W. B., Tiemeyer, M., Wells, L., York, W. S., Zaia, J., Kettner, C., Paulson, J. C., Feizi, T., & Smith, D. F. (2017). The minimum information required for a glycomics experiment (MIRAGE) project: improving the standards for reporting glycan microarray-based data. Glycobiology, 27(4), 280-284. https://doi.org/10.1093/glycob/cww118
Liu, Yan, et al. "The minimum information required for a glycomics experiment (MIRAGE) project: improving the standards for reporting glycan microarray-based data." Glycobiology vol. 27,4 (2017): 280-284. doi: https://doi.org/10.1093/glycob/cww118
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 KH, Kolarich D, Novotny MV, 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 DF. The minimum information required for a glycomics experiment (MIRAGE) project: improving the standards for reporting glycan microarray-based data. Glycobiology. 2017 Apr;27(4):280-284. doi: 10.1093/glycob/cww118. Epub 2016 Nov 22. PMID: 27993942; PMCID: PMC5444268.
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The human gut symbiont Ruminococcus gnavus shows specificity to blood group A antigen during mucin glycan foraging: Implication for niche colonisation in the gastrointestinal tract.

PLoS biology

Wu H, Crost EH, Owen CD, van Bakel W, Martínez Gascueña A, Latousakis D, Hicks T, Walpole S, Urbanowicz PA, Ndeh D, Monaco S, Sánchez Salom L, Griffiths R, Reynolds RS, Colvile A, Spencer DIR, Walsh M, Angulo J, Juge N.
PMID: 34936658
PLoS Biol. 2021 Dec 22;19(12):e3001498. doi: 10.1371/journal.pbio.3001498. eCollection 2021 Dec.

The human gut symbiont Ruminococcus gnavus displays strain-specific repertoires of glycoside hydrolases (GHs) contributing to its spatial location in the gut. Sequence similarity network analysis identified strain-specific differences in blood-group endo-β-1,4-galactosidase belonging to the GH98 family. We determined the...

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Wu H, Crost EH, Owen CD, et al. The human gut symbiont Ruminococcus gnavus shows specificity to blood group A antigen during mucin glycan foraging: Implication for niche colonisation in the gastrointestinal tract. PLoS Biol. 2021;19(12):e3001498doi: 10.1371/journal.pbio.3001498.
Wu, H., Crost, E. H., Owen, C. D., van Bakel, W., Martínez Gascueña, A., Latousakis, D., Hicks, T., Walpole, S., Urbanowicz, P. A., Ndeh, D., Monaco, S., Sánchez Salom, L., Griffiths, R., Reynolds, R. S., Colvile, A., Spencer, D. I. R., Walsh, M., Angulo, J., & Juge, N. (2021). The human gut symbiont Ruminococcus gnavus shows specificity to blood group A antigen during mucin glycan foraging: Implication for niche colonisation in the gastrointestinal tract. PLoS biology, 19(12), e3001498. https://doi.org/10.1371/journal.pbio.3001498
Wu, Haiyang, et al. "The human gut symbiont Ruminococcus gnavus shows specificity to blood group A antigen during mucin glycan foraging: Implication for niche colonisation in the gastrointestinal tract." PLoS biology vol. 19,12 (2021): e3001498. doi: https://doi.org/10.1371/journal.pbio.3001498
Wu H, Crost EH, Owen CD, van Bakel W, Martínez Gascueña A, Latousakis D, Hicks T, Walpole S, Urbanowicz PA, Ndeh D, Monaco S, Sánchez Salom L, Griffiths R, Reynolds RS, Colvile A, Spencer DIR, Walsh M, Angulo J, Juge N. The human gut symbiont Ruminococcus gnavus shows specificity to blood group A antigen during mucin glycan foraging: Implication for niche colonisation in the gastrointestinal tract. PLoS Biol. 2021 Dec 22;19(12):e3001498. doi: 10.1371/journal.pbio.3001498. eCollection 2021 Dec. PMID: 34936658; PMCID: PMC8730463.
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mAb Das-1 recognizes 3'-Sulfated Lewis A/C, which is aberrantly expressed during metaplastic and oncogenic transformation of several gastrointestinal Epithelia.

PloS one

Brown JW, Das KK, Kalas V, Das KM, Mills JC.
PMID: 34910746
PLoS One. 2021 Dec 15;16(12):e0261082. doi: 10.1371/journal.pone.0261082. eCollection 2021.

INTRODUCTION: Multiple previous studies have shown the monoclonal antibody Das-1 (formerly called 7E12H12) is specifically reactive towards metaplastic and carcinomatous lesions in multiple organs of the gastrointestinal system (e.g. Barrett's esophagus, intestinal-type metaplasia of the stomach, gastric adenocarcinoma, high-grade...

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Brown JW, Das KK, Kalas V, et al. mAb Das-1 recognizes 3'-Sulfated Lewis A/C, which is aberrantly expressed during metaplastic and oncogenic transformation of several gastrointestinal Epithelia. PLoS One. 2021;16(12):e0261082doi: 10.1371/journal.pone.0261082.
Brown, J. W., Das, K. K., Kalas, V., Das, K. M., & Mills, J. C. (2021). mAb Das-1 recognizes 3'-Sulfated Lewis A/C, which is aberrantly expressed during metaplastic and oncogenic transformation of several gastrointestinal Epithelia. PloS one, 16(12), e0261082. https://doi.org/10.1371/journal.pone.0261082
Brown, Jeffrey W, et al. "mAb Das-1 recognizes 3'-Sulfated Lewis A/C, which is aberrantly expressed during metaplastic and oncogenic transformation of several gastrointestinal Epithelia." PloS one vol. 16,12 (2021): e0261082. doi: https://doi.org/10.1371/journal.pone.0261082
Brown JW, Das KK, Kalas V, Das KM, Mills JC. mAb Das-1 recognizes 3'-Sulfated Lewis A/C, which is aberrantly expressed during metaplastic and oncogenic transformation of several gastrointestinal Epithelia. PLoS One. 2021 Dec 15;16(12):e0261082. doi: 10.1371/journal.pone.0261082. eCollection 2021. PMID: 34910746; PMCID: PMC8673611.
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Glycoconjugates in host-helminth interactions.

Frontiers in immunology

Prasanphanich NS, Mickum ML, Heimburg-Molinaro J, Cummings RD.
PMID: 24009607
Front Immunol. 2013 Aug 28;4:240. doi: 10.3389/fimmu.2013.00240. eCollection 2013.

Helminths are multicellular parasitic worms that comprise a major class of human pathogens and cause an immense amount of suffering worldwide. Helminths possess an abundance of complex and unique glycoconjugates that interact with both the innate and adaptive arms...

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Prasanphanich NS, Mickum ML, Heimburg-Molinaro J, et al. Glycoconjugates in host-helminth interactions. Front Immunol. 2013;4:240doi: 10.3389/fimmu.2013.00240.
Prasanphanich, N. S., Mickum, M. L., Heimburg-Molinaro, J., & Cummings, R. D. (2013). Glycoconjugates in host-helminth interactions. Frontiers in immunology, 4240. https://doi.org/10.3389/fimmu.2013.00240
Prasanphanich, Nina Salinger, et al. "Glycoconjugates in host-helminth interactions." Frontiers in immunology vol. 4 (2013): 240. doi: https://doi.org/10.3389/fimmu.2013.00240
Prasanphanich NS, Mickum ML, Heimburg-Molinaro J, Cummings RD. Glycoconjugates in host-helminth interactions. Front Immunol. 2013 Aug 28;4:240. doi: 10.3389/fimmu.2013.00240. eCollection 2013. PMID: 24009607; PMCID: PMC3755266.
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Human group A rotavirus P[25] VP8* specifically binds to A-type histo-blood group antigen.

Virology

Li D, Wang M, Qi J, Zhang Q, Wang H, Pang L, Sun X, Duan Z.
PMID: 33453651
Virology. 2021 Mar;555:56-63. doi: 10.1016/j.virol.2020.12.016. Epub 2021 Jan 05.

Rotavirus (RV) is a common cause of acute gastroenteritis in young children. While P[8] and P[4] are the most prevalent RV genotypes in humans, other genotypes are also reported in human infections occasionally, including human P[25]. The glycan binding...

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Li D, Wang M, Qi J, et al. Human group A rotavirus P[25] VP8* specifically binds to A-type histo-blood group antigen. Virology. 2021;555:56-63doi: 10.1016/j.virol.2020.12.016.
Li, D., Wang, M., Qi, J., Zhang, Q., Wang, H., Pang, L., Sun, X., & Duan, Z. (2021). Human group A rotavirus P[25] VP8* specifically binds to A-type histo-blood group antigen. Virology, 55556-63. https://doi.org/10.1016/j.virol.2020.12.016
Li, Dandi, et al. "Human group A rotavirus P[25] VP8* specifically binds to A-type histo-blood group antigen." Virology vol. 555 (2021): 56-63. doi: https://doi.org/10.1016/j.virol.2020.12.016
Li D, Wang M, Qi J, Zhang Q, Wang H, Pang L, Sun X, Duan Z. Human group A rotavirus P[25] VP8* specifically binds to A-type histo-blood group antigen. Virology. 2021 Mar;555:56-63. doi: 10.1016/j.virol.2020.12.016. Epub 2021 Jan 05. PMID: 33453651.
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Profiling of core fucosylated N-glycans using a novel bacterial lectin that specifically recognizes α1,6 fucosylated chitobiose.

Scientific reports

Vainauskas S, Duke RM, McFarland J, McClung C, Ruse C, Taron CH.
PMID: 27678371
Sci Rep. 2016 Sep 28;6:34195. doi: 10.1038/srep34195.

A novel fucose-binding lectin (SL2-1) from the bacterium Streptomyces rapamycinicus was identified by analysis of metagenomic DNA sequences. SL2-1 belongs to a new group of bacterial fucose-specific lectins that have no similarity to known bacterial fucose-binding proteins, but are...

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Vainauskas S, Duke RM, McFarland J, et al. Profiling of core fucosylated N-glycans using a novel bacterial lectin that specifically recognizes α1,6 fucosylated chitobiose. Sci Rep. 2016;6:34195doi: 10.1038/srep34195.
Vainauskas, S., Duke, R. M., McFarland, J., McClung, C., Ruse, C., & Taron, C. H. (2016). Profiling of core fucosylated N-glycans using a novel bacterial lectin that specifically recognizes α1,6 fucosylated chitobiose. Scientific reports, 634195. https://doi.org/10.1038/srep34195
Vainauskas, Saulius, et al. "Profiling of core fucosylated N-glycans using a novel bacterial lectin that specifically recognizes α1,6 fucosylated chitobiose." Scientific reports vol. 6 (2016): 34195. doi: https://doi.org/10.1038/srep34195
Vainauskas S, Duke RM, McFarland J, McClung C, Ruse C, Taron CH. Profiling of core fucosylated N-glycans using a novel bacterial lectin that specifically recognizes α1,6 fucosylated chitobiose. Sci Rep. 2016 Sep 28;6:34195. doi: 10.1038/srep34195. PMID: 27678371; PMCID: PMC5039751.
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Humanization of JAA-F11, a Highly Specific Anti-Thomsen-Friedenreich Pancarcinoma Antibody and InVitro Efficacy Analysis.

Neoplasia (New York, N.Y.)

Tati S, Fisk JC, Abdullah J, Karacosta L, Chrisikos T, Philbin P, Morey S, Ghazal D, Zazala F, Jessee J, Quataert S, Koury S, Moreno D, Eng JY, Glinsky VV, Glinskii OV, Sesay M, Gebhard AW, Birthare K, Olson JR, Rittenhouse-Olson K.
PMID: 28830009
Neoplasia. 2017 Sep;19(9):716-733. doi: 10.1016/j.neo.2017.07.001. Epub 2017 Aug 19.

JAA-F11 is a highly specific mouse monoclonal to the Thomsen-Friedenreich Antigen (TF-Ag) which is an alpha-O-linked disaccharide antigen on the surface of ~80% of human carcinomas, including breast, lung, colon, bladder, ovarian, and prostate cancers, and is cryptic on...

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Tati S, Fisk JC, Abdullah J, et al. Humanization of JAA-F11, a Highly Specific Anti-Thomsen-Friedenreich Pancarcinoma Antibody and InVitro Efficacy Analysis. Neoplasia. 2017;19(9):716-733doi: 10.1016/j.neo.2017.07.001.
Tati, S., Fisk, J. C., Abdullah, J., Karacosta, L., Chrisikos, T., Philbin, P., Morey, S., Ghazal, D., Zazala, F., Jessee, J., Quataert, S., Koury, S., Moreno, D., Eng, J. Y., Glinsky, V. V., Glinskii, O. V., Sesay, M., Gebhard, A. W., Birthare, K., Olson, J. R., & Rittenhouse-Olson, K. (2017). Humanization of JAA-F11, a Highly Specific Anti-Thomsen-Friedenreich Pancarcinoma Antibody and InVitro Efficacy Analysis. Neoplasia (New York, N.Y.), 19(9), 716-733. https://doi.org/10.1016/j.neo.2017.07.001
Tati, Swetha, et al. "Humanization of JAA-F11, a Highly Specific Anti-Thomsen-Friedenreich Pancarcinoma Antibody and InVitro Efficacy Analysis." Neoplasia (New York, N.Y.) vol. 19,9 (2017): 716-733. doi: https://doi.org/10.1016/j.neo.2017.07.001
Tati S, Fisk JC, Abdullah J, Karacosta L, Chrisikos T, Philbin P, Morey S, Ghazal D, Zazala F, Jessee J, Quataert S, Koury S, Moreno D, Eng JY, Glinsky VV, Glinskii OV, Sesay M, Gebhard AW, Birthare K, Olson JR, Rittenhouse-Olson K. Humanization of JAA-F11, a Highly Specific Anti-Thomsen-Friedenreich Pancarcinoma Antibody and InVitro Efficacy Analysis. Neoplasia. 2017 Sep;19(9):716-733. doi: 10.1016/j.neo.2017.07.001. Epub 2017 Aug 19. PMID: 28830009; PMCID: PMC5565633.
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mAb Das-1 recognizes 3'-Sulfated Lewis A/C, which is aberrantly expressed during metaplastic and oncogenic transformation of several gastrointestinal Epithelia.

PloS one

Brown JW, Das KK, Kalas V, Das KM, Mills JC.
PMID: 34910746
PLoS One. 2021 Dec 15;16(12):e0261082. doi: 10.1371/journal.pone.0261082. eCollection 2021.

INTRODUCTION: Multiple previous studies have shown the monoclonal antibody Das-1 (formerly called 7E12H12) is specifically reactive towards metaplastic and carcinomatous lesions in multiple organs of the gastrointestinal system (e.g. Barrett's esophagus, intestinal-type metaplasia of the stomach, gastric adenocarcinoma, high-grade...

Cite
Brown JW, Das KK, Kalas V, et al. mAb Das-1 recognizes 3'-Sulfated Lewis A/C, which is aberrantly expressed during metaplastic and oncogenic transformation of several gastrointestinal Epithelia. PLoS One. 2021;16(12):e0261082doi: 10.1371/journal.pone.0261082.
Brown, J. W., Das, K. K., Kalas, V., Das, K. M., & Mills, J. C. (2021). mAb Das-1 recognizes 3'-Sulfated Lewis A/C, which is aberrantly expressed during metaplastic and oncogenic transformation of several gastrointestinal Epithelia. PloS one, 16(12), e0261082. https://doi.org/10.1371/journal.pone.0261082
Brown, Jeffrey W, et al. "mAb Das-1 recognizes 3'-Sulfated Lewis A/C, which is aberrantly expressed during metaplastic and oncogenic transformation of several gastrointestinal Epithelia." PloS one vol. 16,12 (2021): e0261082. doi: https://doi.org/10.1371/journal.pone.0261082
Brown JW, Das KK, Kalas V, Das KM, Mills JC. mAb Das-1 recognizes 3'-Sulfated Lewis A/C, which is aberrantly expressed during metaplastic and oncogenic transformation of several gastrointestinal Epithelia. PLoS One. 2021 Dec 15;16(12):e0261082. doi: 10.1371/journal.pone.0261082. eCollection 2021. PMID: 34910746; PMCID: PMC8673611.
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Identification of Lectins from Metastatic Cancer Cells through Magnetic Glyconanoparticles.

Israel journal of chemistry

Kavunja HW, Voss PG, Wang JL, Huang X.
PMID: 27110035
Isr J Chem. 2015 Mar 01;55(3):423-436. doi: 10.1002/ijch.201400156. Epub 2015 Mar 23.

Cancer cells can have characteristic carbohydrate binding properties. Previously, it was shown that a highly metastatic melanoma cell line B16F10 bound to galacto-side-functionalized nanoparticles much stronger than the corresponding less metastatic B16F1 cells. To better understand the carbohydrate binding...

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Kavunja HW, Voss PG, Wang JL, et al. Identification of Lectins from Metastatic Cancer Cells through Magnetic Glyconanoparticles. Isr J Chem. 2015;55(3):423-436doi: 10.1002/ijch.201400156.
Kavunja, H. W., Voss, P. G., Wang, J. L., & Huang, X. (2015). Identification of Lectins from Metastatic Cancer Cells through Magnetic Glyconanoparticles. Israel journal of chemistry, 55(3), 423-436. https://doi.org/10.1002/ijch.201400156
Kavunja, Herbert W, et al. "Identification of Lectins from Metastatic Cancer Cells through Magnetic Glyconanoparticles." Israel journal of chemistry vol. 55,3 (2015): 423-436. doi: https://doi.org/10.1002/ijch.201400156
Kavunja HW, Voss PG, Wang JL, Huang X. Identification of Lectins from Metastatic Cancer Cells through Magnetic Glyconanoparticles. Isr J Chem. 2015 Mar 01;55(3):423-436. doi: 10.1002/ijch.201400156. Epub 2015 Mar 23. PMID: 27110035; PMCID: PMC4838199.
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Presentation Modality of Glycoconjugates Modulates Dendritic Cell Phenotype.

Biomaterials science

Hotaling NA, Ratner DM, Cummings RD, Babensee JE.
PMID: 26146546
Biomater Sci. 2014 Oct 01;2(10):1426-1439. doi: 10.1039/C4BM00138A.

The comparative dendritic cell (DC) response to glycoconjugates presented in soluble, phagocytosable, or non-phagocytosable display modalities is poorly understood. This is particularly problematic, as the probing of immobilized glycans presented on the surface of microarrays is a common screen...

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Hotaling NA, Ratner DM, Cummings RD, et al. Presentation Modality of Glycoconjugates Modulates Dendritic Cell Phenotype. Biomater Sci. 2014;2(10):1426-1439doi: 10.1039/C4BM00138A.
Hotaling, N. A., Ratner, D. M., Cummings, R. D., & Babensee, J. E. (2014). Presentation Modality of Glycoconjugates Modulates Dendritic Cell Phenotype. Biomaterials science, 2(10), 1426-1439. https://doi.org/10.1039/C4BM00138A
Hotaling, N A, et al. "Presentation Modality of Glycoconjugates Modulates Dendritic Cell Phenotype." Biomaterials science vol. 2,10 (2014): 1426-1439. doi: https://doi.org/10.1039/C4BM00138A
Hotaling NA, Ratner DM, Cummings RD, Babensee JE. Presentation Modality of Glycoconjugates Modulates Dendritic Cell Phenotype. Biomater Sci. 2014 Oct 01;2(10):1426-1439. doi: 10.1039/C4BM00138A. PMID: 26146546; PMCID: PMC4486352.
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Deciphering the glycogenome of schistosomes.

Frontiers in genetics

Mickum ML, Prasanphanich NS, Heimburg-Molinaro J, Leon KE, Cummings RD.
PMID: 25147556
Front Genet. 2014 Aug 05;5:262. doi: 10.3389/fgene.2014.00262. eCollection 2014.

Schistosoma mansoni and other Schistosoma sp. are multicellular parasitic helminths (worms) that infect humans and mammals worldwide. Infection by these parasites, which results in developmental maturation and sexual differentiation of the worms over a period of 5-6 weeks, induces...

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Mickum ML, Prasanphanich NS, Heimburg-Molinaro J, et al. Deciphering the glycogenome of schistosomes. Front Genet. 2014;5:262doi: 10.3389/fgene.2014.00262.
Mickum, M. L., Prasanphanich, N. S., Heimburg-Molinaro, J., Leon, K. E., & Cummings, R. D. (2014). Deciphering the glycogenome of schistosomes. Frontiers in genetics, 5262. https://doi.org/10.3389/fgene.2014.00262
Mickum, Megan L, et al. "Deciphering the glycogenome of schistosomes." Frontiers in genetics vol. 5 (2014): 262. doi: https://doi.org/10.3389/fgene.2014.00262
Mickum ML, Prasanphanich NS, Heimburg-Molinaro J, Leon KE, Cummings RD. Deciphering the glycogenome of schistosomes. Front Genet. 2014 Aug 05;5:262. doi: 10.3389/fgene.2014.00262. eCollection 2014. PMID: 25147556; PMCID: PMC4122909.
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