GeoMx® DSP: What Surprised This Early Adopter Most
During her post doc years, Trieu My Van explored the effects of immuno check point blockade in melanoma patients, comparing samples from metastatic uveal and cutaneous melanoma tissues at the whole exome, transcriptional and proteomic level. With GeoMx DSP and the ability to to simultaneously and spatially multiplex protein and gene erxpression on a single FFPE tissue, she identified an immune exhausted state in metastatic uveal melanoma and a greater dependency on PD-L1 immune check point in cutaneous melanoma, thus explaining the different response to immune therapy in these 2 tumor types.
She was indeed one of our very first GeoMx® DSP users, and she loved it.
What was the most surprising thing about using the GeoMx DSP platform?
I was quite surprised about the high amount of data that’s coming out of the platform from only a single FFPE tissue. This allows us to get better insight into our tumor tissues.
What about GeoMx DSP do you think makes it an ideal platform to define candidate novel biomarkers in your research?
We think that the major advantages of this platform are its high multiplexing ability that allows us to better characterize our tumor tissues, low hands-on time, and non-destructive working steps.
Why is the non-destructive nature important for your studies?
Since we are a cancer institute, we are focusing mainly on tissue biopsies for research. These biopsies are mostly limited and, therefore, quite precious. This platform allows us to reuse them for further DSP analysis and also for HE or IC stains.
How has the experience been as a beta user?
It has been a great experience to be one of the first people working on this new platform. Already at this stage it advances our standard analysis of our tumor tissues a lot.
What tips do you have for others interested in using the platform?
Since it’s a novel platform not many guidelines are established for ROI selection or data analysis. In our recently published review, we provided some guidelines based on our own experience.
What aspect of the software did you find interesting/useful?
We are working in the immune-oncology field; therefore, we are focusing mainly on the immune infiltrations in tumor samples. For our analysis, the segmentation tool is quite useful since we can focus mainly on our immune infiltrates within the tumor area.
What was your experience combining the imaging and profiling data sets?
It was an advantage for us to use fluorescently labeled morphology markers to guide our analysis specifically to focus on immune infiltrates and their surrounding environment.
What added value does analyzing BOTH protein and RNA bring to your study?
If we don’t have the right antibody for protein DSP we can still use RNA DSP to enable these analyses. At the same time, having the results from the DSP protein and the RNA DSP further validates the outcome of the results.
If GeoMx DSP was not available, how would you go about getting this information?
When we are focusing mainly on the protein we would need to apply different techniques like Western blotting, proteomics or FACS analysis. However, these techniques lack the ability to provide us with spatial information and, therefore, it requires additional standard IC analysis. However, if we want to have this high multiplexing ability, we’d need to have many sections from one biopsy. GeoMx DSP is a game changer.
*For Research Use Only. Not for use in diagnostic procedures.