Glycomics


Glycomics is the comprehensive study of glycomes, including genetic, physiologic, pathologic, and other aspects. Glycomics "is the systematic study of all glycan structures of a given cell type or organism" and is a subset of glycobiology. The term glycomics is derived from the chemical prefix for sweetness or a sugar, "glyco-", and was formed to follow the omics naming convention established by genomics and proteomics.

Challenges

This area of research has to deal with an inherent level of complexity not seen in other areas of applied biology. 68 building blocks provide the structural basis for the molecular choreography that constitutes the entire life of a cell. DNA and RNA have four building blocks each. Lipids are divided into eight categories based on ketoacyl and isoprene. Proteins have 20. Saccharides have 32 types of sugar linkages. While these building blocks can be attached only linearly for proteins and genes, they can be arranged in a branched array for saccharides, further increasing the degree of complexity.
Add to this the complexity of the numerous proteins involved, not only as carriers of carbohydrate, the glycoproteins, but proteins specifically involved in binding and reacting with carbohydrate:
To answer this question one should know the different and important functions of glycans. The following are some of those functions:
There are important medical applications of aspects of glycomics:
Glycomics is particularly important in microbiology because glycans play diverse roles in bacterial physiology. Research in bacterial glycomics could lead to the development of:
The following are examples of the commonly used techniques in glycan analysis

High-resolution mass spectrometry (MS) and high-performance liquid chromatography (HPLC)

The most commonly applied methods are MS and HPLC, in which the glycan part is cleaved either enzymatically or chemically from the target and subjected to analysis. In case of glycolipids, they can be analyzed directly without separation of the lipid component.
N-glycans from glycoproteins are analyzed routinely by high-performance-liquid-chromatography after tagging the reducing end of the sugars with a fluorescent compound.
A large variety of different labels were introduced in the recent years, where 2-aminobenzamide, anthranilic acid, 2-aminopyridin, 2-aminoacridone and 3--6-aminoacridine are just a few of them.
O-glycans are usually analysed without any tags, due to the chemical release conditions preventing them to be labeled.
Fractionated glycans from high-performance liquid chromatography instruments can be further analyzed by MALDI-TOF-MS to get further information about structure and purity. Sometimes glycan pools are analyzed directly by mass spectrometry without prefractionation, although a discrimination between isobaric glycan structures is more challenging or even not always possible. Anyway, direct MALDI-TOF-MS analysis can lead to a fast and straightforward illustration of the glycan pool.
In recent years, high performance liquid chromatography online coupled to mass spectrometry became very popular. By choosing porous graphitic carbon as a stationary phase for liquid chromatography, even non derivatized glycans can be analyzed. Electrospray ionisation is frequently used for this application.

Multiple Reaction Monitoring (MRM)

Although MRM has been used extensively in metabolomics and proteomics, its high sensitivity and linear response over a wide dynamic range make it especially suited for glycan biomarker research and discovery. MRM is performed on a triple quadrupole instrument, which is set to detect a predetermined precursor ion in the first quadrupole, a fragmented in the collision quadrupole, and a predetermined fragment ion in the third quadrupole. It is a non-scanning technique, wherein each transition is detected individually and the detection of multiple transitions occurs concurrently in duty cycles. This technique is being used to characterize the immune glycome.
Table 1:Advantages and disadvantages of mass spectrometry in glycan analysis
AdvantagesDisadvantages

  • Applicable for small sample amounts
  • Useful for complex glycan mixtures.
  • Attachment sides can be analysed by tandem MS experiments.
  • Glycan sequencing by tandem MS experiments.
  • Destructive method.
  • Need of a proper experimental design.

    • Arrays

    Lectin and antibody arrays provide high-throughput screening of many samples containing glycans. This method uses either naturally occurring lectins or artificial monoclonal antibodies, where both are immobilized on a certain chip and incubated with a fluorescent glycoprotein sample.
    Glycan arrays, like that offered by the Consortium for Functional Glycomics and , contain carbohydrate compounds that can be screened with lectins or antibodies to define carbohydrate specificity and identify ligands.

    Metabolic and covalent labeling of glycans

    Metabolic labeling of glycans can be used as a way to detect glycan structures. A well known strategy involves the use of azide-labeled sugars which can be reacted using the Staudinger ligation. This method has been used for in vitro and in vivo imaging of glycans.

    Tools for glycoproteins

    and nuclear magnetic resonance spectroscopy for complete structural analysis of complex glycans is a difficult and complex field. However, the structure of the binding site of numerous lectins, enzymes and other carbohydrate-binding proteins has revealed a wide variety of the structural basis for glycome function. The purity of test samples have been obtained through chromatography and analytical electrophoresis.

    Software and databases

    There are several on-line software and databases available for glycomic research. This includes: