Tutorial:

1. Introduction

CD (cluster of differentiation) antigens are cell surface-expressed antigens defined by monoclonal antibodies. The great value of the CD nomenclature is to provide a unified system of classified antigens useful both for biological research and clinical practice. The CD antigens are expressed on human hematopoietic cells but also to some extent on endothelial and epithelial cells. During the decades the CD system has been developed, the information provided for a specific antigen has become more and more complex expanding from just cellular and tissue expression to biochemical structure, genetic background and to its functional impact in a given cellular environment. Most of the CD antibodies recognize the protein moiety of surface, membrane integral macromolecules, but some of them detect oligosaccharide structures, which are linked to either glycoproteins or glycosphingolipids. Access to the complexity of knowledge about CD antigens in times of www-based data storage at the moment not available. This GlycoCD database now endeavours to keep abreast with nowadays bioinformational standards giving in-depth information about glycan CD antigens and those CD-defined surface receptors (lectins), which bind to glycan structures.

2. Carbohydrate and lectin CD

During the International Workshop and Conference on Human Leucocyte Differentiation Antigens (HLDA) 2000 in Harrogate a separate workshop on carbohydrate and lectin CDs was established considering the increasing interest and research advance in unravelling cellular protein-glycan interactions. The objective was to initiate a more comprehensive compilation of monoclonal antibody-defined carbohydrate structures and lectins differentially expressed on human leukocytes and to provide an appropiate classification within the CD nomenclature. Since this conference our knowledge about lectin interactions has gained considerable progress. In order to establish this GlycoCD database we have collected actual information on glycan and lectin CDs from the literature available and other online resources and compiled these data. We have separated these data inside the GlycoCD database into two section: carbohydrate recognition CD antigens and glycan CDs.

3. GlycoCD database

GlycoCD is a collection of lectins and carbohydrates defined by CD antibodies which are differentially expressed primarily on human leukocytes but also on certain endothelial and epithelial cells. The databank comprises information on 63 CD antigens (out of 363 of total CD antigens as defined in 2012) and each glycan CD is related to glycan array data giving information about possible protein binding partners wherever available. Furthermore, links to other relevant databases are provided. For the convenience of the users glycan related CDs can be searched either by the respective CD number or the glycan specificity.

Home page of GlycoCD databank:


3.1 Carbohydrate recognition CD

The carbohydrate recognition CD section contains:
1. lectin CDs which are classified within distinct lectin families such as selectins or siglecs
2. CD antigens outside lectin families which have a carbohydrate recognition domain (CRD) defined by sequence homologies. For some of these, a functional influence of the CRD has not yet been clarified.
3. CD proteins which are related to carbohydrate binding in that interactions with glycan moieties of other antigens influence their functional activities. You can search these data from the “Browse menu”. Each set of data in this section contains information about synonyms of this particular CD protein, its structure (also, where available, 3dimensional), amino acid and nucleic acid sequence, cellular and tissue expression, function (and clinical application), carbohydrate and other possible ligands, further links to glycan array data.

Browse page:

This page is for searching carbohydrate related CDs. Users can search by CD number. On top right corner there is a drop down list of molecules/non GlycoCDs, which interact with GlycoCDs. User can select these molecules from drop down list and check interactions by clicking check interaction button.


This bottom section of browse page for searching carbohydrate related CDs by glycan specificity.


Data page:

This page is for detailed information about CDs. It contains general information, different ids information from different databases, sequence information, carbohydrate microarray data information, and references. In carbohydrate microarray information, it is linked to two databases; Consortium of functional glycomics (CFG) database, and Glyaffinity database.


Glycan array page:


Glycan array data from glyaffinity database:

For example, here CD62P (P-selectin) glycan array data are shown. It contains 3 measurements. These three measurements are different with regard to concentration, used for glycan screening. Glycan structure depicted in sets of measurements have been measured highest at highest affinity towards P-selectin. You can acheived more information by clicking Details.


Glycan array data from CFG database:

From CFG database, Users can retrieve information on experimental details, download glycan array raw data, and see glycans from interactive chart as shown in figure below.


3.2 Glycan CD

Glycan CDs which define oligosacchride moeities linked to glycoproteins and/or glycosphingolipids. Users can search glycan CDs data under search by CD. Each set of data in this section contains information about their structural representation (Glycotope), synonyms, molecular structure, function, expression, application,ligand (CD binding), other linked structure databases, glycan array data, and references.

The term “Glycotope” defines the minimal carbohydrate sequence recognized by a given CD antibody. If this glycotope is unequivocally expressed as part of a glycolipid (e.g. CD17, CD60a,b,c, CD77) we have added in “molecular structure” –Cer (ceramide). In other cases we have added an –R in order to express that this minimal glycotope is part of a larger antigen (either glycoprotein or glycolipid and/or longer oligosaccharide chain of the entire antigen).

Glycan CD information:


Other structure databases:

This is the page of GlycomeDB database: -a unified database for carbohydrate structures.It is linked to several other carbohydrate structure databases.


Glycan array data:

This is the page of Glyaffinity database: -a repository for carbohydrate microarrays. In the left column of the page showing name of experiment and the right coloumn is displaying affinity detected/not detected. Users can ignore those experiment which are showing affinity not detected for this carbohydrate.


4. Other important resources

HCDM Portal

Uniprot Portal

Wiki Portal

ebioscience portal

PathologyOutlines.com

The Immunology Link

5. Some relevant reviews on the CD system in general

1. Schwartz-Albiez, R. (2009) Inflammation and Glycosciences. In, The sugar code. Gabius,H.; Wiley-VCH, Weinheim, Germany, pp447-463.

2. Beare, A., Stockinger, H., Zola, H. and Nicholson, I. (2008) Monoclonal antibodies to human cell surface antigens, Curr Protoc Immunol, Appendix 4, 4A. Pubmed

3. Zola H, Swart B, Banham A, Barry S, Beare A, Bensussan A, Boumsell L, C DB, Buhring HJ, Clark G et al: CD molecules 2006--human cell differentiation molecules. J Immunol Methods 2007, 319(1-2):1-5. Pubmed

4. Zola, H. and Swart, B. (2005) The human leucocyte differentiation antigens (HLDA) workshops: the evolving role of antibodies in research, diagnosis and therapy, Cell Res, 15, 691-694. Pubmed

5. Zola, H., Swart, B., Nicholson, I., Aasted, B., Bensussan, A., Boumsell, L., Buckley, C., Clark, G., Drbal, K., Engel, P., Hart, D., Horejsi, V., Isacke, C., Macardle, P., Malavasi, F., Mason, D., Olive, D., Saalmueller, A., Schlossman, S.F., Schwartz-Albiez, R., Simmons, P., Tedder, T.F., Uguccioni, M. and Warren, H. (2005) CD molecules 2005: h uman cell differentiation molecules, Blood, 106, 3123-3126. Pubmed

6. Schwartz-Albiez, R. and Kniep, B. (2005) Perspectives for establishment and reorganization of carbohydrate-directed CD antibodies. Report of the carbohydrate section, Cell Immunol, 236, 48-50. Pubmed

7. Mason, D., Andre, P., Bensussan, A., Buckley, C., Civin, C., Clark, E., de Haas, M., Goyert, S., Hadam, M., Hart, D., Horejsi, V., M euer, S., Morrissey, J., Schwartz-Albiez, R., Shaw, S., Simmons, D., Uguccioni, M., van der Schoot, E., Vivier, E. and Zola, H. (2002) CD antigens 2002, Blood, 99, 3877-3880. Pubmed

8. Mason, D. et al. (2002) Leucocyte Typing VII. Oxford University Press, Oxford.

9. Barclay et al. (1997) The Leucocyte Antigen Factsbook, Second Edition, Academic Press, San Diego, California, USA.

10. Schwartz-Albiez, R. (2002) Carbohydrates and lectins. In, Leucocyte Typing VII. University Press, Oxford, pp147-206.

11. Zola et al. (2007) Leukocyte and Stromal Cell Molecules: The CD Markers, John Wiley & Sons, Inc., Hoboken, New Jersey.