e15185 Background: Solid tumor specimen collection during clinical trials often follows a standard histology protocol, ending in the generation of FFPE sections mounted onto 1 mm histology slides. Though a common sample format for researchers developing tissue-based biomarkers, slides present a data quality challenge for multiplexed spatial biology workflows. Here we present data describing an innovative flow cell design fully compatible with pre-slided tissue specimens. We collected spatial biology data using this slide-compatible flow cell and compared it to the gold standard direct mounting on coverglass. Several rounds of marker staining and imaging demonstrate equivalency in method outcomes including image resolution, signal to noise, and re-interrogation capacity. Methods: FFPE biopsy tissue specimens (tumor punch biopsies and a tonsil section) were mounted on standard histology slides. These specimens were incorporated into flow cells using a new glass coverslip and porting device, CellScape™ Slide, that pairs with a standard histology slide to form a microfluidic chamber. After mounting, each sample was probed for consensus CD markers (CD45, CD3, CD4,CD8,CD20, etc.) through several rounds of iterative immunofluorescence staining using CellScape™ Precise Spatial Multiplexing. The resulting multi-layered whole slide image dataset was then interrogated for spatial resolution and signal-to-noise using digital image analysis. Results: Spatial resolution and signal-to-noise ratio (SNR) were assessed through comparison to data collected from similar samples using the existing CellScape microfluidic chip. The lowest intensity signal collected with at least a 30:1 SNR (acceptable for image analysis) was equivalent or lower in the CellScape Slide preparation (equivalent sensitivity). The highest intensity signal collected was equivalent between the two flow cell designs. Comparing stain quality (specificity, sensitivity) among markers stained through multiple rounds of iterative staining, imaging, and signal remove via photoinactivation showed that the CellScape Slide flow cell is on par with or better than the existing CellScape chip. Further, the usable clear window of the CellScape Slide flow chamber, measuring 16 mm x 44 mm, was found to be greater than twice that of the existing chip. Literature review determined this to also be the largest imaging window available among commercially available spatial biology platforms. Conclusions: Assessment of the CellScape Slide flow cell, innovative in providing access to the CellScape spatial biology workflow for pre-mounted FFPE tissue, determined that the optical performance of the new flow cell is at least on par with the existing flow cell. Further, the usable window is over twice the area, and the new flow cell is fully capable of supporting re-interrogation of the sample.
Read full abstract