Research Consortium Develops New Tool for Biology
By Jason Socrates Bardi
An international consortium of scientists led by Professor James Paulson of The Scripps Research Institute has created a technology that will advance our understanding of the role of complex sugar chains (glycans or carbohydrates) that decorate the surface of cells in the body. The technology, known as a functional glycan microarray, is a glass slide onto which are printed hundreds of different glycan chains.
The array offers scientists a cutting edge research tool allowing them to analyze the specificities of glycan binding proteins (GBP's), which function through their binding to such sugar chains.
The microarray will transform research in the burgeoning field of glycomics, which is devoted to the systematic identification and characterization of all the glycan structures produced by organisms. This field is a necessary component in understanding human health because of the importance of glycans as key players in all the body's functions. However, progress in elucidating this information and determining the biological functions of complex carbohydrates has lagged behind advances in the related fields of genomics (concerned with DNA, RNA and genes) and proteomics (concerned with proteins).
Many proteins involved in communication between cells recognize glycan structures on cell surfaces. The functional glycan microarray will speed research in glycomics, because it will allow scientists to determine to which carbohydrate structures these proteins bind.
"Any glycan-binding protein can be studied," says Paulson. "They all work."
The Scripps Research scientist Ola Blixt led this development together with Steve Head, the Director of Scripps Research DNA Microarray Core. Blixt, Head, and their colleagues developed the glycan array using a standard microarray printing technology analogous to an ink jet printer to arrange the sugars onto glass slides.
The arrays, which are described in an upcoming issue of the journal Proceedings of the National Academy of Sciences, were developed under the auspices of the Consortium for Functional Glycomics (CFG).
In its present format the printed glycan array was established by the carbohydrate synthesis core which is directed by Blixt and coordinated by Paulson and Chi-Huey Wong, the Ernest W. Hahn Professor and Chair in Chemistry and an investigator in The Skaggs Institute for Chemical Biology at The Scripps Research Institute. The Consortium in which Paulson serves as Director and Principal Investigator, is funded by a $37 million "glue" grant awarded by the National Institute of General Medical Sciences, one of the National Institutes of Health and has brought together some 160 independently funded researchers at 110 different institutions around the world, including several in San Diego, with the goal of understanding how proteins in the body bind to carbohydrates and how these interactions mediate cell functions.
Carbohydrates in Life and On Glass
Carbohydrate structures are very much a part of the language of life. They are like the accents on spoken words—they change the meaning without changing the spelling. Some even call carbohydrates the third alphabet, behind DNA and proteins.
Glycosylation, the attachment of carbohydrate chains to proteins, is a crucial part of biology, and some scientists estimate that half of all proteins encoded by the human genome get sugars attached to them at some point after they are made. All cells, foreign and human, are covered with carbohydrates, and some viruses, like HIV and influenza, use sugars on the outside of human cells to gain entry into human cells.
Though they are not charged with storing genetic information like DNA or acting as enzymatic workhorses like proteins, carbohydrates nevertheless do carry information and are responsible for important biological functions, playing a central role in many types of intercellular communication events, protein folding, cell adhesion, and immune recognition.
One of the most important frontiers of basic research in biology today is to understand the human glycome—all of the types of carbohydrate structures in the human body and what they do. This is a profoundly difficult endeavor. The total number of carbohydrate structures in humans may be 10,000 to 20,000, although it is hard to fix a hard number to this, says Paulson. Nevertheless, he adds, "We think understanding the glycome is possible now. We didn't think that three years ago."
Unlike genomics and proteomics, no high-throughput tools to study glycomics have existed. The need for tools to speed up this research is paramount. Several groups of scientists have attempted to make glycan arrays in the last few years, but the number of sugars in the arrays and the number of proteins that could be applied to the arrays were limited.
Several laboratories in the NIGMS-funded consortium have collaborated to create a new glycan array, which will make it easier and faster to determine how a diversity of human glycan binding proteins interact with carbohydrates in biological systems. Over the last few years, consortium scientists have constructed a library of more than 200 biologically relevant sugars.
In an upcoming issue of the journal Proceedings of the National Academy of Sciences, Blixt, Paulson, and their colleagues report that they have developed a simple way to permanently array sugars onto glass slides. Using standard commercially available technology, sugars that have been given an "amino linker" are printed onto slides coated with a chemically reactive surface and become covalently attached. The array of more than 200 different sugar structures can be expanded as additional sugars become available.
"This array covers all the major types of terminal sugars," says Paulson. He notes that for the majority of glycan structures, their "inner core" portion, is the same in all cells and tissues. What varies are the terminal sequences of sugars, the last few end sugars on the carbohydrate chain. Proteins that bind to carbohydrates only recognize the last few sugars in a carbohydrate chain, and perhaps as few as 500 or so of these terminal sequences in nature are relevant.
Members of the consortium tested the new microarray on a variety of glycan binding proteins from humans and other organisms. They also looked at the carbohydrate binding properties of a complete virus, which suggests that the arrays may be able to define the carbohydrate-binding specificity for whole viruses as well as viral proteins.
Finally, the scientists successfully looked at the carbohydrate binding properties of antibodies using the array, suggesting this new tool may be developed into a powerful diagonistic screen for evidence of antibodies in human blood that would indicate a bacterial or viral infection, a hidden cancer, or an emerging autoimmune disease.
The article, "Printed Covalent Glycan Array for Ligand Profiling of Diverse Glycan Binding Proteins" is authored by Ola Blixt, Steve Head, Tony Mondala, Christopher Scanlan, Margaret E. Huflejt, Richard Alvarez, Marian C. Bryan, Fabio Fazio, Daniel Calarese, James Stevens, Nahid Razi1, David J. Stevens, John J. Skehel, Irma van Die, Dennis R. Burton, Ian A. Wilson, Richard Cummings, Nicolai Bovin, Chi-Huey Wong, and James C. Paulson and is available online at: http://www.pnas.org/cgi/reprint/0407902101. The article will be published in an upcoming issue of the journal Proceedings of the National Academy of Sciences.
This work was supported by funds from the National Institute of General Medical Sciences, one of the National Institutes of Health.
For more information on the Consortium for Functional Glycomics, see the consortium's home page at: http://functionalglycomics.org.
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