PROJECT SUMMARY The CosMx Spatial Molecular Imaging Platform (CosMxTM SMI, NanoString, Seattle, WA) will allow a well- funded group of biomedical scientists experienced in the application of single cell transcriptomic approaches to human disease to perform combined spatial transcriptomics and proteomics at a cellular and subcellular resolution using tissue samples collected at Northwestern University (NU) and within the greater Chicago area. This is an integrated system with mature cyclic in situ hybridization chemistry, an ultra-high-resolution imaging readout, and interactive data analysis and visualization software. The CosMx™ SMI platform enables the simultaneous quantification and visualization of up to 1,000 RNA and 100 validated protein analytes, allowing cell typing and discovery, neighborhood clustering, phenotyping of the tissue microenvironment and differential expression analysis of cell types and subsets based on spatial location. This disruptive technology will be applied to freshly isolated or paraffin-embedded-and-stored tissues collected as part of clinical care or after causal genetic and pharmacologic interventions in murine models of lung disease. In addition to their fundamental mechanistic work in cell and animal models of disease, the Major Users in this application have pioneered the application of single cell RNA-sequencing approaches to human disease, generating among the largest extant collaborative molecular atlases of human lung disease. They will leverage this knowledge to optimize sample selection, probe design, and morphologic measurements that will maximize the yield from the combined transcriptomic/proteomic and spatial/morphological features of disease uniquely generated by the CosMx™ SMI platform. The machine learning approaches they have developed to integrate single cell transcriptomic data from tens of laboratories across hundreds of individuals and millions of cells will be foundational to analyzing data from the The CosMx™ SMI platform and integrating them within this larger body of work. Thus, by providing this instrument to these users, this Shared Instrument Proposal will accelerate the application of spatial transcriptomics and proteomics to the study of human disease through innovations in clinical phenotyping, sample collection and processing, imaging and cell biology, data science and a commitment to open access data sharing. The CosMxTM SMI will be managed by the Metabolomics Developing Core Facility/Integrative Genomics (MCF-IG) at Robert H. Lurie Cancer Center (RHLCCC) at NU, which supports all major and minor users with LCMS based metabolomics and high throughput integrative genomics to enable integrated analysis of genes and pathways through which metabolism contributes to disease. The core facility physically resides within space provided by the Division of Pulmonary and Critical Care in the Department of Medicine.