Developing Spatialomics Platforms to Profile Biomarkers

Multiplexed mRNA and protein profiling in the spatial context provides important new information enabling basic research and clinical applications. Unfortunately, most existing spatial transcriptomics and proteomics methods are limited due to either low multiplexing or assay complexity. Here, we introduce a new spatialomics technology, termed Multi Omic Single-scan Assay with Integrated Combinatorial Analysis (MOSAICA), that integrates in situ labeling of mRNA and protein markers in cells or tissues with combinatorial fluorescence spectral and lifetime encoded probes, spectral and time-resolved fluorescence imaging, and machine learning-based target decoding. This technology is the first application combining the biophotonic techniques, Spectral and Fluorescence Lifetime Imaging and Microscopy (FLIM), to the field of spatial transcriptomics and proteomics. By integrating the time dimension with conventional spectrum-based measurements, MOSAICA enables direct and highly multiplexed in situ spatial biomarker profiling in a single round of staining and imaging while providing error correction removal of background autofluorescence. We demonstrated MOSAICA’s capabilities in cell culture and Formalin-Fixed Paraffin-Embedded (FFPE) tissues while obtaining a strong correlation with sequencing data (Pearson’s r = 0.96). We then demonstrate simultaneous co-detection of protein and mRNA in colorectal cancer cells. To answer biological questions with a simple 3-4 plex immunofluorescence panel, we developed a low-cost Tissue Imager for under $9,000 and achieved a performance on par with commercial fluorescence microscopes that cost ~20x more. Additionally, another tool we developed to study the tissue microenvironment was cell-based mechanosensors to quantitively and dynamically assess the tissue mechanics. We have already used MOSAICA to study colon cancer heterogeneity, profile neurological mRNA panels in brain tissue, and profile immuno-oncology panels for skin tissue. MOSAICA represents a simple, versatile, and scalable tool for targeted spatial transcriptomics and proteomics analysis that can find broad utility in constructing human cell atlases, elucidating biological and disease processes in the spatial context, and serving as companion diagnostics for stratified patient care