Region of interest localization, tissue storage time, and antibody binding density-a technical note on the GeoMx® Digital Spatial Profiler

Background: Spatial biology is an emerging concept to interrogate tumor heterogeneity. The NanoString GeoMx® Digital Spatial Profiling (DSP) platform has become increasingly available. It combines high-plex analysis of protein or messenger RNA expression using barcoded antibodies or oligonucleotide probes with investigator-driven selection of regions of interest. Cell populations, e.g. immune cells, can be selectively analyzed via segmentation. A key advantage is the use of archived formalin-fixed, paraffin-embedded tissue, however, begging the question whether and to what extent tissue fixation and storage time affect the results.

Materials and methods: Antibody binding density (ABD), i.e. the number of barcodes/μm², is a key quality control measure for DSP spatial proteomics. To assess whether regional differences in tissue fixation have an influence on ABD, we compared 652 regions of interest selected from tumor center and periphery of 49 prostate cancer and 25 renal cell carcinoma (RCC) specimens. Moreover, the effect of tissue storage time on ABD was examined. Finally, we tested whether regional differences have an influence on ABD of segmented CD45+ or CD8+ cells.

Results: No significant differences in ABD between tumor center and periphery were found in prostate cancer or RCC. However, ABD was significantly higher in recent specimens (≤5 years) when compared with those that were older (>5 years; P = 0.027). There was a trend towards higher ABD in the tumor periphery of RCC specimens after segmentation for immune cells, albeit without reaching statistical significance.

Conclusions: The NanoString GeoMx® DSP platform delivers robust data to interrogate tumor heterogeneity, but tissue storage time should be considered when interpreting the results.