Tumours are cellular ecosystems that originate from distinct lineages and differentiate into a multitude of cellular subtypes or states. The spatial organisation of cells in tumours has been demonstrated to be not only a projection of the molecular nature of cancer but also an important predictor for the progression of the tumour and response to treatments. Conventional spatial technologies such as multiplexed immunofluorescence can only examine a handful of markers at a time, restricting our ability to comprehensively map the cellular and molecular features of tumours in tissue.
Several technologies have emerged to solve this challenge. Among these technologies, the GeoMX Digital Spatial Profiling (DSP) platform from Nanostring and the Visium platform from 10X Genomics have emerged as two powerful spatial transcriptomic tools with high data dimensionality and relatively high throughput. While both platforms have been demonstrated to generate robust outputs across a spectrum of tissues with high reproducibility, these two platforms vary substantially in experimental workflow and method of data collection. Previous comparisons of these two platforms are often based on data generated in unmatched samples without directly comparing technical features between the two platforms.
To bridge this gap, we have evaluated the performance of the GeoMX DSP and Visium platforms on matched synthetic cell pellets and clinical primary breast cancer patient samples. The former sample type consists of cell lines mixed at different ratios providing a well-controlled system for the direct technical comparison, while the latter extends our comparisons to a more practical setting. We applied the DSP, Visium fresh frozen (FF) and recently released Visium Formalin-Fixed Paraffin-Embedded (FFPE) solutions to serial sections from blocks preserved as FF or FFPE. This not only allows a direct comparison between these technologies but also provides insight into the effect of sample preservation on data quality. With the direct comparison between the DSP and Visium platforms, we provide a practical guide to prospective users of these technologies with technical comparisons, insights on experimental workflow and data processing to assist in decision-making when considering spatial transcriptomic experiments.