Precise spatial multiplexing of protein biomarkers for immune profiling in tissue samples with ChipCytometry™

Immunohistochemistry is the most widely used diagnostic technique in tissue pathology. However, IHC is associated with several limitations including the labeling of just a few markers per tissue section and limited quantification of cell populations. As a result of plex limitations, key insights about tumor biology are missed, which could be important for advancing our understanding of tumor biology and ultimately improving patient outcomes. ChipCytometry™ is a novel image-based platform for precise spatial multiplexing that addresses these challenges by combining iterative immuno-fluorescent staining with high-dynamic range imaging to facilitate quantitative phenotyping with single-cell resolution. The platform enables simultaneous detection of dozens of markers on a single tissue section and enables accurate quantification of protein expression levels necessary to deeply profile single cells, understand interactions between key immune cells, and identify topographic biomarkers. Here we demonstrate how standard FCS files are generated from multichannel OME-TIFF images, enabling identification of cellular phenotypes via flow cytometry-like hierarchical gating. Quantification of results reveal precise expression levels for each marker in the assay in each individual cell in the sample, while maintaining spatial information about each cell. ChipCytometry has the potential to advance precision medicine in immuno-oncology and inform the discovery of novel biomarkers by enabling quantitative analysis of cellular phenotypes in the spatial context. The ChipCytometry platform enables simultaneous detection of multiple protein markers on a single tissue section for deep immune cell profiling in the tumor microenvironment. Combined with the single-cell spatial information, such data sets provide an opportunity for the discovery of new complex multiplexed biomarker signatures to inform therapeutic development.