What is Glycomics?

The term "glycome" is used to refer to the entire glycan (carbohydrate) component - free (uncombined) as well as combined - present in the living cells of organisms. ^[1]

Glycomics is thus defined as the systematic study of the glycan structures present in any living cell.

Glycomics not only involves the study of carbohydrates alone, but also deals with the study of carbohydrates combining or being associated with other macromolecules - lectins, glycoproteins, glycolipids, enzymes specific for carbohydrates, cell receptors specific for carbohydrates, sugar molecules present in nucleic acids, etc. ^[2]

Glycomics is regarded as one of the most complex entities to be studied in the living cell.

Need for studying Glycomics ^{[3] [4]}

Carbohydrates are one the most abundant macromolecules present in living organisms. They are highly complex biomolecules present in the following forms - unbound (free), chain, branched, bound, conjugated, etc.

Glycan molecules are extremely critical for the proper functioning of the living cell. Their functions can be broadly given as follows -

1. Glycans represent the largest and potentially the most versatile natural resource present on the Earth. They are a diverse source of chemicals, fuel, food, organic materials, etc.

2. Plant cell walls are chiefly made of cellulose. Cellulose can be used as biomass as well as an inexpensive and sustainable source of biofuel.

3. Glycan-based materials can also be used for the synthesis of animal feed.

4. Glycans are involved in cell-signalling pathways.

5. Glycans are actively involved in the immune system in the form of complement components.

6. Glycocalyx is the substance that covers all living cells and polysaccharides are present on the outer surface of prokaryotic cells.

7. Glycans can affect the metastatic potential of cancerous cells as well as replication of viruses.

8. Glycans play a crucial role in the determination of the ABO blood grouping system.

9. Glycoscience is an area of biology which is linked to all other disciplines -

• Physiology and Developmental Biology - Glycans play an important role in tissue development
• Medicine and Pathology - Glycoproteins present on surfaces of bacterial cells and viral components are involved in the occurrence of various diseases.
• Microbiology - Study of interactions between various microorganisms as well as microorganisms and other cells.
• Chemistry - Development of newer techniques for the study and analysis of glycans and other carbohydrate-associated molecules.
• Biochemistry - Study of role of glycans in various metabolic pathways and the occurrence of metabolic disorders.

Protein glycosylation is one of the forms of post-translational modifications occurring during protein synthesis.

N-linked glycans play an important role in protein folding.

• Materials Science - Synthesis of carbohydrate-based polymers having a wide range of uses.
• Computational Science - Study and analysis of the interactions between the in-silico models of various sugars with other moieties for better understanding of the functioning of glycans.

Tools used for Glycomics study ^{[5] [6]}

1. Mass Spectroscopy - Glycan is cleaved enzymatically or chemically from the target molecule and analyzed. If the glycan molecule being analyzed is a glycolipid, the analysis can be carried out without the separation of the lipid component of the molecule.

The main advantages of using Mass Spectroscopy as a tool for glycomic analysis are that it can detect concentrations of glycans present in minute quantities (range of lower fmol). Also, complex glycan molecules can also be detected and analyzed using this tool.

2. High Performance Liquid Chromatography (HPLC) - N- and O-glycans are analyzed using HPLC (all three types) after attaching a fluorescent tag at that end of the sugar molecule which undergoes reduction. The tags that can be used for labeling the sugar molecule are anthranilic acid, 2-aminobenzamide, etc.

3. Carbohydrate Microarrays

   ♦ High-mannose microarrays - Synthetically created or naturally occurring glycan libraries are immobilized on various solid surfaces, and are analyzed for further studies. However, lack of mobility remains a concern with the usage of solid surfaces as microarrays. To counter this problem, a fluid microarray or whole cell microarrays are deemed to be more suitable for glycan analysis.

   ♦ Antibiotic microarrays - Aminoglycosides are glycan molecules which are used as broad-spectrum antibiotics. Aminoglycosides function as antibiotics by binding to the ribosomes of bacteria, and thereby, preventing or blocking protein synthesis. However, the effectiveness of the action of aminoglycosides as antibiotics has decreased due to antibiotic resistance.

Antibiotic microarrays can be used to analyze those compounds that cause antibiotic resistance, as well as to identify newer glycan-based antibiotics.

   ♦ Hybrid carbohydrate/glycoprotein microarrays - Glycoproteins are those glycan molecules which contain a protein moiety. These microarrays can be used for studying the protein-protein interactions in a glycoprotein molecule, alongwith the glycan-protein interaction.

   ♦ Microsphere arrays - These are artificially constructed optical microarrays which are internally encoded so as to detect the structure and position of carbohydrates present in a glycan molecule.

To detect the presence of a glycan molecule bound to any other moiety, a carbohydrate-binding protein is taken which is a labeled with a fluorophore molecule. This is incubated alongwith the immobilized microsphere array. The binding between the microarray and the fluorophore-labelled moiety is analyzed by measuring the fluorescence and the wavelength through an internal coding that acts as a marker for the glycan molecule.

4. Metabolic and covalent labeling - This tool is used for the detection of the presence of glycan structures. Glycan molecules are labelled with azides or substrates containing azido groups. Once the reaction takes place between the azide group and the glycan molecule, in-vivo and in-vitro changes in the glycan molecule can be detected and studied using fluorescence microscopy.

This tool provides information about the type of glycan molecule present, as well as its bonding with the azide group.

5. X-ray crystallography and Nuclear Magnetic Resonance (NMR) spectroscopy - These techniques are used for performing a structural analysis of complex glycan molecules. Glycans with structural and functional attributes such as lectins, enzymes acting on sugar moieties, glycoproteins, etc., can be studied using these techniques.

The structures of the glycans present in these molecules can be confirmed using methods such as chromatography, analytical electrophoresis, etc.

6. Surface Plasmon Resonance (SPR) - The binding of glycans to different types of ligands in real-time can be studied using the technique of SPR. Both low-affinity as well as high-affinity interactions can be studied using this tool.

A solution containing the glycan-bound ligand is washed over a surface. The bound ligand accumulates on the surface, the refractive index of the surface is measured before as well as after the accumulation of the ligand, and the change in the refractive index is noted.

Self-Assembled Monolayers (SAMs) can be used which offer a control over the density of the immobilized glycan-bound ligand accumulated on the surface.

7. Fluorescent Carbohydrate Conjugates

   ♦ Monosaccharide oligosaccharide fluorophore constructs - The valency of a lectin molecule is directly proportional to the interactions between the glycan molecules and the receptor protein residues. This principle has been traditionally analyzed using cell-based and solid phase assays.

A newer method has been designed for glycomic analysis for studying the interaction between the saccharide and the protein. Monovalent oligosaccharide-fluorophore conjugates are taken so as to observe the affinity of the lectin molecule to the oligosaccharide conjugate in a specific solution. The affinity or valency displayed by the lectin molecule is studied as part of glycomic analysis.

   ♦ Multivalent oligosaccharide platforms - To analyze multivalent interactions, a semiconductor nanocrystal (quantum-dot based system) is taken so as to offer multiple points of interaction between the oligosaccharide residue and the lectin molecule.

8. Carbohydrate Affinity Screening - Synthetically constructed agents can be used to isolate carbohydrate residues from crude mixtures. Some of the synthetic constructs include latex beads, magnetic particles, resins of agarose and sepaharose, etc.

These constructs are modified in such a way so as to display affinity for specific oligosaccharides. Specific matrices derivatized from saccharides can be used to isolate the simpler carbohydrate-binding proteins. However, in the case of complex carbohydrate-binding proteins, simultaneous activity takes place - isolation of the glycan moiety as well as determination of its structural specificity.

Applications of Glycomics ^{[7] [8]}

1. Medical field and Clinical Diagnosis -

→ Development of glycotherapeutic compounds through post-translational modifications, as well as therapy for other processes such as inflammation, infection, neurodegeneration, etc.

→ Glycomics can also be used for the detection of ovarian cancer and liver sclerosis, discovery of new glycodiagnostics, identification of serum glycoprotein biomarkers helping in disease detection, etc.

2. Applications of Bacterial Glycomics -

→ Metabolic oligosaccharide labeling and engineering for studying complex glycan structures in bacteria

• Synthesis of bioactive glycans
• Glycoconjugate vaccines

→ Study of the role of glycans in treating infectious diseases caused by bacteria

Current Research ^{[9] [10]}

1. Differences in the levels of serum glycan can be used as a means of detecting gastric cancer. It implies that glycomics may be used as a marker for the detection of the disease.

2. Marine glycans obtained from red seaweed can be used in skincare products as they act against adverse effects of excessive sunlight exposure to the skin. These products can also be used as alternatives to botox.

References -

[1] http://en.wikipedia.org/wiki/Glycomics

[2] http://www.griffith.edu.au/science-aviation/institute-glycomics/about-us/what-is-glycomics

[3] http://en.wikipedia.org/wiki/Glycomics#Importance

[4] http://www.ncbi.nlm.nih.gov/books/NBK109958/pdf/TOC.pdf

[5] http://en.wikipedia.org/wiki/Glycomics#Tools_used

[6] http://tinyurl.com/ofrbbvl

[7] http://pubs.acs.org/doi/pdf/10.1021/pr801057j

[8] http://www.horizonpress.com/glycomics

[9] http://tinyurl.com/nkvzpbc

[10] http://www.prweb.com/releases/2014/01/prweb11479268.htm