Visualizing in situ single-cell multi-omic gene expression from FFPE Tissue with MERSCOPE

In order to truly understand cell biology, researchers need easy-to-use tools that preserve the natural complexity of tissues while capturing the nuances of gene and protein expression. Vizgen’s in situ single-cell genomics platform MERSCOPE™, built on multiplexed error robust in situ hybridization (MERFISH) technology, enables the direct profiling of the spatial organization of intact tissue with subcellular resolution. To date, MERSCOPE measurements have been limited to RNA detection only and restricted to fresh frozen and fixed frozen tissue samples. Here we describe two new applications of Vizgen’s MERSCOPE platform: protein co-detection and FFPE (formalin-fixed paraffin-embedded) sample processing. To enable protein co-detection on MERSCOPE, we developed the MERSCOPE Protein Stain Kits which employ oligo-conjugated secondary antibodies and a specialized blocking reagent to co-detect protein targets together with Vizgen’s MERFISH technology. We demonstrated co-detection of common protein cell markers with hundreds of RNAs quantified in human colon cancer sections, mouse brain sections, and U2OS cell line cultures. Data outputs were further analyzed through visualization using the MERSCOPETM Vizualizer software.

 

To further expand MERSCOPE compatible sample types, we introduced the MERSCOPE FFPE Sample Prep Kit and MERSCOPE FFPE Slides which feature a new robust sample preparation process to enable downstream MERFISH measurements from FFPE tissues. Using the new FFPE MERSCOPE products and an upgraded CellPose cell segmentation algorithm we were able to systematically characterize the gene expression among cells across multiple human tissue samples.

 

Finally, we demonstrated successful co-detection of proteins within FFPE samples, highlighting the synergistic power of these two protocols to interrogate aspects of human disease.

 

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