Investigating the role of glypicans in cancer

Glypicans are a group of proteoglycans, macromolecules consisting of a core protein and attached carbohydrate chains. We interviewed our customer who studies glypicans’ involvement in cancer and neurodegenerative disease, and their potential as diagnostic or prognostic markers. The Genevia team is helping her to take advantage of cancer databases in her research.

(This customer prefers to remain anonymous.)

After medical studies and spending a year in a clinic in central Sweden, this researcher returned to the university to start her career in research in 1996. Since then, she’s been a full-time research scientist working in the field of cell biology.

– I got my PhD in 2001, and continued my research in the same laboratory. Now I have a professorship and I’m doing basic research on proteoglycans. They are proteins with carbohydrate chains, and we are looking at their role in disease development in cancers and neurodegenerative disease, both of which are riddled with problems related to the accumulation of damaged proteins, she explains.

In particular, the researcher’s lab is interested in a group of six proteoglycans called glypicans. The researcher says there is a lot of published data showing that these six proteins are differentially expressed in cancers. For example, glypican 3 is observed to be abundant in kidney cancer, and less expressed in other types of cancer.

– I thought that maybe we could use bioinformatics and have a closer look at the expression profiles with the help of cancer databases, and if we see that there is a correlation between the high or low expressions in different cancers, maybe glypicans could be used as diagnostic or prognostic factors. In addition, there are antibodies to these proteins, so later on they might also be treatment target candidates.

The timing could not have been better when almost at the same time that the researcher got awarded a grant for her cancer research, she also got an email from Genevia inquiring if she might have needs for bioinformatics support. She had little experience on bioinformatics herself, and was only familiar with a few databases.

– I was thinking of hiring a postdoc or starting a collaboration with some other group. When Antti [Genevia’s CEO] contacted me, I figured that maybe this might be a quicker way to kick the project off, and also a way to kind of keep it to myself instead of sharing it with some other researcher, she explains the decision to outsource.

– I talked to Antti, and he told me that they could have a look at The Cancer Genome Atlas. The start of the collaboration went very well: Antti explained how everything would work, and then assigned me a project manager, Grigorios Georgolopoulos, to work with. We are now working on the manuscripts together, and have received some very interesting results. Of course, some parts of the results have not always been as interesting or useful as we expected, but there is a lot of data. The project is not finished yet, and if only we can afford it, we want to continue the collaboration.

Data transfers and communication via email and video meetings have been working smoothly, and the customer has been especially happy with the fast service and quick response rate.

– Grigorios has gone through the data very carefully, and he is so easy to work with and good at explaining everything. I can only say positive things. The service is fast and we can always discuss what kind of help I can get: for example, I’m getting help in making the figures for the manuscript, and now that I’m writing, I may ask Grigorios to read it and make sure that my assumptions are correct and not taken too far. I get a lot of value for the time that I’m charged for.

– Often when I talk with people about my cancer projects, their reaction is “How are you going to do that?” and then I get to tell them that I am collaborating with this company called Genevia. Usually they find it quite interesting, she smiles.

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