Search

Mixed-lineage Acute Leukemia (MLL) is one of the most high-risk forms of pediatric cancer. Although the long-term survival rates of pediatric acute lymphoblastic leukemia have increased over the past 40 years, the current chemotherapeutic treatment schemes often fail in the treatment of MLL. The biological mechanisms resulting in drug resistance, however, are still not fully understood and there is an urgent need to identify novel diagnostic and therapeutical targets. We have established the first integrated multi-omics investigation of primary patient MLL samples and control precursor B bonemarrow cells from healthy donors, mapping their proteome, transcriptome and glycome. 4–6 million cells from 3 normal bone marrow (BM) and 2 MLL samples were used for analysis on our multi-omics platform. Porous-Graphitised Carbon (PGC) nanoLC-ESIMS/MS was used for Glycomics analyses after the enzymatic and chemical release of N- and O-glycans, respectively. The proteome was explored using RP-LC-ESI-MS/MS analyses, performed after offline high-pH fractionation, in addition to RNA-seq analyses. Overall, 4225 proteins were identified across the patient MLL and control BM cells, of which 216 were overexpressed in MLL (p 2). Preliminary analyses of the RNA-seq data matched well with the proteomics findings, revealing significant alterations in expression of glycoprotein signalling receptors and extracellular matrix proteins as well as various transcription factors. High-pH fractionation also allowed us to identify numerous important glycosyltransferases and expression changes thereof on protein and RNA– seq level. N- and O-glycomics revealed overall lower levels of α2–6 sialylated N- and O-glycans in MLL cells (correlating with ST6Gal1 transcript and ST6Gal1 protein levels) as well as an increase in Core 2 type O-glycans (correlating with GCNT1 transcript level). Patient MLL cells exhibit distinct N- and O-glycan fingerprints, along with specific alterations of receptor tyrosine kinase signalling networks. In addition to wellknown MLL glycoprotein markers, our integrated multiomics workflow identified a number of diagnostic/therapeutic protein candidates that have not previously been described.

The Minimum Information Required for a Glycomics Experiment (MIRAGE) is an initiative created by experts in the fields of glycobiology, glycoanalytics and glycoinformatics to design guidelines that improve the reporting and reproducibility of glycoanalytical methods. Previously, the MIRAGE Commission has published guidelines for describing sample preparation methods and the reporting of glycan array and mass spectrometry techniques and data collections. Here, we present the first version of guidelines that aim to improve the quality of the reporting of liquid chromatography (LC) glycan data in the scientific literature. These guidelines cover all aspects of instrument setup and modality of data handling and manipulation and is cross-linked with other MIRAGE recommendations. The most recent version of the MIRAGE-LC guidelines is freely available at the MIRAGE project website doi:10.3762/mirage.4.

The minimum information required for a glycomics experiment (MIRAGE) project was established in 2011 to provide guidelines to aid in data reporting from all types of experiments in glycomics research including mass spectrometry (MS), liquid chromatography, glycan arrays, data handling and sample preparation. MIRAGE is a concerted effort of the wider glycomics community that considers the adaptation of reporting guidelines as an important step towards critical evaluation and dissemination of datasets as well as broadening of experimental techniques worldwide. The MIRAGE Commission published reporting guidelines for MS data and here we outline guidelines for sample preparation. The sample preparation guidelines include all aspects of sample generation, purification and modification from biological and/or synthetic carbohydrate material. The application of MIRAGE sample preparation guidelines will lead to improved recording of experimental protocols and reporting of understandable and reproducible glycomics datasets.

The MIRAGE (minimum information required for a glycomics experiment) initiative was founded in Seattle, WA, in November 2011 in order to develop guidelines for reporting the qualitative and quantitative results obtained by diverse types of glycomics analyses, including the conditions and techniques that were applied to prepare the glycans for analysis and generate the primary data along with the tools and parameters that were used to process and annotate this data. These guidelines must address a broad range of issues, as glycomics data are inherently complex and are generated using diverse methods, including mass spectrometry (MS), chromatography, glycan array-binding assays, nuclear magnetic resonance (NMR) and other rapidly developing technologies. The acceptance of these guidelines by scientists conducting research on biological systems in which glycans have a significant role will facilitate the evaluation and reproduction of glycomics experiments and data that is reported in scientific journals and uploaded to glycomics databases. As a first step, MIRAGE guidelines for glycan analysis by MS have been recently published (Kolarich D, Rapp E, Struwe WB, Haslam SM, Zaia J., et al. 2013. The minimum information required for a glycomics experiment (MIRAGE) project – Improving the standards for reporting mass spectrometry-based glycoanalytic data. Mol. Cell Proteomics. 12:991–995), allowing them to be implemented and evaluated in the context of real-world glycobiology research. In this paper, we set out the historical context, organization structure and overarching objectives of the MIRAGE initiative.

Kiyoko FAoki-Kinoshita1, Hiromichi Sawaki2, Hyun Joo An3, Matthew Campbell4, Qichen Cao5, Richard Cummings6, Daniel K Hsu7, Masaki Kato8, Toshisuke Kawasaki9, Kay-Hooi Khoo7, Jaehan Kim3, Daniel Kolarich10, Xianyu Li5, Mingqi Liu11, Masaaki Matsubara12, Shujiro Okuda9,13, Nicolle H Packer4, Rene Ranzinger14, Huali Shen11, Toshihide Shikanai2, Daisuke Shinmachi2, Philip Toukach15, Issaku Yamada12, Yoshiki Yamaguchi8, Pengyuan Yang11, Wantao Ying5, Jong Shin Yoo16, Yan Zhang17, Yang Zhang11, and Hisashi Narimatsu2 Soka University, Tokyo, Japan; National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan; Chungnam National University, Daejeon, Korea; Macquarie University, Sydney, NSW, Australia; Beijing Institute of Radiation Medicine, Beijing, China; Emory University, Atlanta, GA, USA; Academia Sinica, Taipei, Taiwan; RIKEN Global Research Cluster, Wako-shi, Saitama, Japan; Ritsumeikan University, Kusatsu, Shiga, Japan; Max Planck Institute of Colloids and Interfaces, Potsdam, Germany; Fudan University, Shanghai, China; The Noguchi Institute, Tokyo, Japan; Niigata University, Niigata, Japan; The University of Georgia, Athens, GA, USA; Zelinsky Institute of Organic Chemistry, Moscow, Russia; Korea Basic Science Institute, Daejeon, Korea; and Shanghai Jiao Tong University, Shanghai, China

Protein transport within cereal endosperm cells is complicated by the abundance of endoplasmic reticulum (ER)-derived and vacuolar protein bodies. For wheat storage proteins, two major transport routes run from the ER to the vacuole, one bypassing and one passing through the Golgi. Proteins traveling along each route converge at the vacuole and form aggregates. To determine the impact of this trafficking system on the fate of recombinant proteins expressed in wheat endosperm, we used confocal and electron microscopy to investigate the fate of three recombinant proteins containing different targeting information. KDEL-tagged recombinant human serum albumin, which is retrieved to the ER lumen in leaf cells, was deposited in prolamin aggregates within the vacuole of endosperm cells, most likely following the bulk of endogenous glutenins. Recombinant fungal phytase, a glycoprotein designed for secretion, was delivered to the same compartment, with no trace of the molecule in the apoplast. Glycan analysis revealed that this protein had passed through the Golgi. The localization of human serum albumin and phytase was compared to that of recombinant legumin, which contains structural targeting information directing it to the vacuole. Uniquely, legumin accumulated in the globulin inclusion bodies at the periphery of the prolamin bodies, suggesting a different mode of transport and/or aggregation. Our results demonstrate that recombinant proteins are deposited in an unexpected pattern within wheat endosperm cells, probably because of the unique storage properties of this tissue. Our data also confirm that recombinant proteins are invaluable tools for the analysis of protein trafficking in cereals.

The N-glycans from 27 "plant" foodstuffs, including one from a gymnospermic plant and one from a fungus, were prepared by a new procedure and examined by means of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). For several samples, glycan structures were additionally investigated by size-fractionation and reverse-phase high-performance liquid chromatography in conjunction with exoglycosidase digests and finally also (1)H-nuclear magnetic resonance spectroscopy. The glycans found ranged from the typical vacuolar "horseradish peroxidase" type and oligomannose to complex Le(a)-carrying structures. Though the common mushroom exclusively contained N-glycans of the oligomannosidic type, all plant foods contained mixtures of the above-mentioned types. Apple, asparagus, avocado, banana, carrot, celery, hazelnut, kiwi, onion, orange, pear, pignoli, strawberry, and walnut were particularly rich in Le(a)-carrying N-glycans. Although traces of Le(a)-containing structures were also present in almond, pistachio, potato, and tomato, no such glycans could be found in cauliflower. Coconut exhibited almost exclusively N-glycans containing only xylose but no fucose. Oligomannosidic N-glycans dominated in buckwheat and especially in the legume seeds mung bean, pea, peanut, and soybean. Papaya presented a unique set of hybrid type structures partially containing the Le(a) determinant. These results are not only compatible with the hypothesis that the carbohydrate structures are another potential source of immunological cross-reaction between different plant allergens, but they also demonstrate that the Le(a)-type structure is very widespread among plants.