Spatial transcriptomics is a method that allows researchers to measure and map gene activity in a tissue sample. The Kuijjer group will collaborate with Dr Xavier Tekpli at Oslo University Hospital (OUS) to measure gene expression levels in breast tumor samples.
Could you explain the spatial transcriptomics profiling of breast cancer samples project in a nutshell?
Spatial transcriptomics measures expression levels of genes in tiny regions of the breast tumor sample. These regions generally include about 1-30 cells. This means that we can analyze expression differences and potentially also differences in how gene expression is regulated, while keeping information on where the cells are located within the tumor tissue. This can give useful information on what cell types are present in the tumor and how they might influence one another.
What does this success mean to you and what will the funding make possible?
I am of course very grateful to have received funding for this project. It will allow us to generate some new, firsthand data, in collaboration with Xavier Tekpli at OUS. Ladislav Hovan has just started his postdoctoral fellowship in the group, in which he will develop methods for spatial transcriptomic network modeling. While there are a few publicly available datasets that he plans to use for method development, getting some additional in-house data will boost our sample sizes. Of course, we also hope to find new results in breast cancer that we can link to the patient's clinical data.
What are you most looking forward to about your collaboration with Xavier Tekpli at OUS?
Xavier has expertise in both single-cell and spatial transcriptomics profiling and has strong knowledge and experience both on what is required in terms of sample preparation, on the bioinformatic analysis of the data, and very importantly on breast cancer biology. We are already collaborating with him on several other projects. I am very much looking forward to continuing our discussions—as he is enthusiastic, takes the time to know our methods in full detail, and always gives thoughtful feedback.