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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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Identification of Glycan-Specific Variable Lymphocyte Receptors Using Yeast Surface Display and Glycan Microarrays.

Methods in molecular biology (Clifton, N.J.)

McKitrick TR, Hanes MS, Rosenberg CS, Heimburg-Molinaro J, Cooper MD, Herrin BR, Cummings RD.
PMID: 34870812
Methods Mol Biol. 2022;2421:73-89. doi: 10.1007/978-1-0716-1944-5_5.

The jawless vertebrates (lamprey and hagfish) evolved a novel adaptive immune system with many similarities to that found in the jawed vertebrates, including the production of antigen-specific circulating antibodies in response to immunization. However, the jawless vertebrates use leucine-rich...

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McKitrick TR, Hanes MS, Rosenberg CS, et al. Identification of Glycan-Specific Variable Lymphocyte Receptors Using Yeast Surface Display and Glycan Microarrays. Methods Mol Biol. 2022;2421:73-89doi: 10.1007/978-1-0716-1944-5_5.
McKitrick, T. R., Hanes, M. S., Rosenberg, C. S., Heimburg-Molinaro, J., Cooper, M. D., Herrin, B. R., & Cummings, R. D. (2022). Identification of Glycan-Specific Variable Lymphocyte Receptors Using Yeast Surface Display and Glycan Microarrays. Methods in molecular biology (Clifton, N.J.), 242173-89. https://doi.org/10.1007/978-1-0716-1944-5_5
McKitrick, Tanya R, et al. "Identification of Glycan-Specific Variable Lymphocyte Receptors Using Yeast Surface Display and Glycan Microarrays." Methods in molecular biology (Clifton, N.J.) vol. 2421 (2022): 73-89. doi: https://doi.org/10.1007/978-1-0716-1944-5_5
McKitrick TR, Hanes MS, Rosenberg CS, Heimburg-Molinaro J, Cooper MD, Herrin BR, Cummings RD. Identification of Glycan-Specific Variable Lymphocyte Receptors Using Yeast Surface Display and Glycan Microarrays. Methods Mol Biol. 2022;2421:73-89. doi: 10.1007/978-1-0716-1944-5_5. PMID: 34870812.
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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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Natural and Synthetic Sialylated Glycan Microarrays and Their Applications.

Frontiers in molecular biosciences

McQuillan AM, Byrd-Leotis L, Heimburg-Molinaro J, Cummings RD.
PMID: 31572731
Front Mol Biosci. 2019 Sep 13;6:88. doi: 10.3389/fmolb.2019.00088. eCollection 2019.

This focused chapter serves as a short survey of glycan microarrays that are available with sialylated glycans, including both defined and shotgun arrays, their generation, and their utility in studying differential binding interactions to sialylated compounds, highlighting N-glycolyl (Gc)...

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McQuillan AM, Byrd-Leotis L, Heimburg-Molinaro J, et al. Natural and Synthetic Sialylated Glycan Microarrays and Their Applications. Front Mol Biosci. 2019;6:88doi: 10.3389/fmolb.2019.00088.
McQuillan, A. M., Byrd-Leotis, L., Heimburg-Molinaro, J., & Cummings, R. D. (2019). Natural and Synthetic Sialylated Glycan Microarrays and Their Applications. Frontiers in molecular biosciences, 688. https://doi.org/10.3389/fmolb.2019.00088
McQuillan, Alyssa M, et al. "Natural and Synthetic Sialylated Glycan Microarrays and Their Applications." Frontiers in molecular biosciences vol. 6 (2019): 88. doi: https://doi.org/10.3389/fmolb.2019.00088
McQuillan AM, Byrd-Leotis L, Heimburg-Molinaro J, Cummings RD. Natural and Synthetic Sialylated Glycan Microarrays and Their Applications. Front Mol Biosci. 2019 Sep 13;6:88. doi: 10.3389/fmolb.2019.00088. eCollection 2019. PMID: 31572731; PMCID: PMC6753469.
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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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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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Tools for generating and analyzing glycan microarray data.

Beilstein journal of organic chemistry

Mehta AY, Heimburg-Molinaro J, Cummings RD.
PMID: 32983270
Beilstein J Org Chem. 2020 Sep 10;16:2260-2271. doi: 10.3762/bjoc.16.187. eCollection 2020.

Glycans are one of the major biological polymers found in the mammalian body. They play a vital role in a number of physiologic and pathologic conditions. Glycan microarrays allow a plethora of information to be obtained on protein-glycan binding...

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Mehta AY, Heimburg-Molinaro J, Cummings RD. Tools for generating and analyzing glycan microarray data. Beilstein J Org Chem. 2020;16:2260-2271doi: 10.3762/bjoc.16.187.
Mehta, A. Y., Heimburg-Molinaro, J., & Cummings, R. D. (2020). Tools for generating and analyzing glycan microarray data. Beilstein journal of organic chemistry, 162260-2271. https://doi.org/10.3762/bjoc.16.187
Mehta, Akul Y, et al. "Tools for generating and analyzing glycan microarray data." Beilstein journal of organic chemistry vol. 16 (2020): 2260-2271. doi: https://doi.org/10.3762/bjoc.16.187
Mehta AY, Heimburg-Molinaro J, Cummings RD. Tools for generating and analyzing glycan microarray data. Beilstein J Org Chem. 2020 Sep 10;16:2260-2271. doi: 10.3762/bjoc.16.187. eCollection 2020. PMID: 32983270; PMCID: PMC7492694.
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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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