What are the cell surface proteins called

ETH researchers can use a new method to examine hundreds of cell surface proteins at the same time. With the knowledge gained, more precise diagnoses could be made and more targeted therapies developed in the future.

Not all cancer is the same. Not all forms spread equally quickly in the body or respond to the same drugs. For example, if a woman is diagnosed with breast cancer, it can be crucial to determine the form and stage of the breast cancer so that the cancer can be targeted. In many cases, medicine is not ready today. Standard therapies, to which not all stages and forms of cancer respond, are the rule rather than the exception.

Wanted: New Antibodies

For diagnosis, tissue samples are examined using specific antibodies that bind to certain proteins on the cell surface. For a cancer diagnosis, proteins or protein combinations are detected that are typical for a certain disease. Coupled fluorescent dyes make the antibodies visible on tissue samples. Since there are only a few well-functioning antibodies, the diagnosis is also based on only a few detectable proteins. The diagnosis is then often simply "cancer" - a certain form cannot yet be detected. In order to better differentiate between different stages and forms of cancer, more precise information about the composition of the proteins on the cell surface of the various forms of cancer would be helpful - as would additional functioning antibodies.

The research group led by Bernd Wollscheid, group leader at the Institute for Systems Biology at ETH Zurich, has developed a new method that helps make it easier to develop new and better antibodies. It's called “Cell Surface Capturing” (CSC). This enables the proteins on the cell surface to be specifically recorded. “With the CSC method, we can simultaneously identify a large number of proteins that are on the surface of cells at a certain point in time,” explains Wollscheid. And not only that: CSC also provides information about the proportions in which these proteins occur. Without any antibodies.

Sugar on the protein surface makes it possible

The overall view of the cell surface and the proteins gathered there is made possible by a few tricks: "So that we can take a closer look at the surface proteins, we use the fact that they are practically all glycoproteins," says Wollscheid. These proteins carry at least one sugar molecule somewhere. The researchers attach a kind of adapter to these sugar molecules, which is firmly attached to the sugar residue. In the next step, all the glycoproteins in the entire cell are cut into small pieces using an enzyme that works like molecular scissors. With the matching counterpart to the adapter, the researchers can then easily fish out all those protein pieces that are attached to the sugar residues, i.e. come from the cell surface. In this way, the researchers obtained pieces of the labeled surface proteins. Before they can be identified, the residual sugar and adapter must be cut off with the help of another enzyme.

The researchers then analyze their collection of protein pieces in the mass spectrometer and obtain data on the structure and quantity of the pieces. “With the help of databases, we can identify the associated proteins and obtain a list of all those proteins that were found on the cell surface at a certain point in time,” explains Wollscheid. In some, the researchers were surprised to find them on the cell surface, as they were not known to be there at all. It is also fascinating that so many proteins can be detected at the same time.

Aiming for more detailed diagnoses

Where previously four to five proteins and their corresponding antibodies had to be sufficient to characterize a body cell or cancer form, cells can now be described in terms of the composition of their entire surface proteins. In order to differentiate between different cell types or cancer forms or stages, differences in the amount and type of proteins on the cell surface can be searched for. In the future, this will enable particularly typical surface proteins to be selected for medical diagnostics and a specific set of antibodies to be developed for them.

The protein pieces obtained with the CSC technology have another decisive advantage: Because they come from the outside of the protein, they are easily accessible to the antibodies and therefore particularly suitable as target structures for antibodies, an idea that was recently patented could. Because of this, they are now used in the production of antibodies.

Testing tissues for medical applications directly using the mass spectrometry-based CSC method is currently out of the question. Tissue samples taken from the patient always contain different cells in different amounts. In addition to cancer cells, the samples also contain healthy cells and cells of the immune system, which falsify the result. Research is therefore carried out with specially enriched tissue samples or with cell cultures that mainly consist of one type of cell. Today, mass spectrometers are not yet sensitive enough to be able to analyze the tiny amounts of protein that could be obtained from individual cells. Antibodies are therefore still needed.

Develop targeted drugs

If the surface properties of certain cancer cells are known, it will also be easier to develop new drugs that are only effective against this one cell type. “Medicines would be conceivable that, due to the surface proteins, only bind to certain cancer cells and render them harmless,” explains Wollscheid. Extreme caution is required: If the drug is not specific enough and destroys all kidney cells in addition to all breast cancer cells, nothing will be gained with the therapy.

Track cell development

If the CSC method catches on, not only medicine but also basic research will benefit from it. By taking several “snapshots” of the cell surface at specific time intervals, the researchers can observe how the protein composition on the cells changes over time. The systems biologists working with Wollscheid were able to demonstrate this using the example of stem cells, which specialized in brain cells. "The composition of the surface proteins changed drastically," says Wollscheid, summarizing the results. In this way, healthy cells can be compared with sick cells, stem cells can be compared with differentiated cells and the development from one form to the other can be followed using the CSC method.

It is quite possible that, with the newly acquired knowledge and the new diagnostic possibilities, tailor-made therapies for cancer patients will be developed in the foreseeable future. However, a lot of research and development work is required before this goal can be achieved.

Literature:

Wollscheid B, Bausch-Fluck D, Henderson C, O’Brien R, Bibel M, Schiess R, Aebersold R, Watts J D: Mass-spectrometric identification and relative quantification of N-linked cell surface glycoproteins. Nat Biotechnol. 2009 Apr; 27 (4): 378-86. Epub 2009 Apr 6. doi: 10.1038 / nbt.1532.