Comparison of CosMx and GeoMx profiling performed on the same human kidney tissues [CosMx]

Spatial transcriptomic profiling enables precise quantification of gene expression with simultaneous localization of expression profiles onto tissue structures. This new technology promises to improve our understanding of the disease mechanisms. Therefore, there is intense interest in applying these methods in clinical trials or as laboratory developed tests to aid in diagnosis of disease. Before these applications can been more broadly deployed in clinical research and diagnostics, it is necessary to thoroughly understand the technology’s performance in real world conditions. In this study, we vet technical reproducibility, data normalization methods and assay sensitivity of digital spatial profiling, one widely used spatial transcriptomic methodology. Using clinically sourced human tissue specimens, we find that digital spatial profiling exhibits high rigor and reproducibility. Our approach lays the foundation for incorporation of digital spatial profiling methods into clinical workflows. Tissues were collected in deidentified fashion with approval of the University of Washington’s IRB Study 1297. Fresh human kidney tissues were sourced from patient’s undergoing nephrectomy for removal of kidney tumors. Samples of uninvolved kidney (4 donors), and a portion of the kidney tumor (renal cell carcinoma, RCC; 1 donor) were fixed in 10% neutral buffered formalin for 24-48 hours and then transferred to 70% ethanol for another 24 hours. Samples from all 4 donors (5 pieces of tissue) were paraffin embedded into a single multi-tissue block prior to sectioning. We profiled this tissue block for both digital spatial profiling (GeoMx DSP) and single molecular imaging (CosMx SMI). We aimed to test the rigor and reproducibility of GeoMx DSP and compare its performance against CosMx SMI.