Multi-omic 3D tissue maps for a Human BioMolecular Atlas

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PROJECT ABSTRACT Spatially resolved molecular maps of mammalian organs hold significant promise in providing a deeper understanding of human organ functioning in health and disease states. Fundamental to this is an understanding how tissue organization impacts on the state of a cell and performance of its function. The overarching goal of the Human BioMolecular Atlas Program (HuBMAP) and specifically of Tissue Mapping Centers within the HuBMAP framework is to generate high-resolution three dimensional (3D) human tissue maps. Present state-of-the-art spatially-resolved tissue analysis assays (e.g. MERFISH, seq- FISH, imaging mass cytometry) utilize antibody-based or oligo probe-based approaches that require prior knowledge of the biomolecular targets to map, challenging the ability to characterize the terra incognita (i.e. the unknown) in a tissue mapping effort. Mass spectrometry (MS)-based omic mapping technologies enable unbiased detection and mapping of metabolites, lipids, and proteins (including post-translational modifications - PTMs) in situ in tissue samples with high-resolution and represents an excellent complement to highly multiplexed targeted approaches for spatially resolved tissue analysis. The overall objective of this application is to generate high-resolution, multi-omic, 3D biomolecular maps of non-diseased human organs. We will take a Google Maps-type approach with our mapping effort progressing in phases to generate reference maps at increasing resolution. First, single-cell or near-single-cell resolution MS-based mapping technologies will be used to provide an unbiased view of tissue molecular spatial architecture. Second, biomolecules of interest will be subsequently interrogated with highly multiplexed sub- cellular resolution spatial omics assays in a targeted fashion. Our focus will be on the pancreas, an essential organ important for several metabolic functions. Notably, the pancreas, despite its importance, is not one of the listed key tissues and organs currently being analyzed by the HuBMAP consortium further supporting the need to focus on this critical organ. We will employ high resolving power and high-resolution mass spectrometry-based molecular mapping platforms (LMD-nanoPOT-MS, MALDI-FTMS, nanoDESI-MS) for unbiased mapping of metabolites, lipids, and proteins (including PTMs such as phosphorylation). These MS assays will be complemented with powerful highly multiplexed targeted spatial omics assays (CODEX and NanoString GeoMx for protein and RNA respectively) and light sheet microscopy to generate high-resolution, multi-omics human tissue maps. The innovative spatially resolved multi-omic tissue maps generated will be unprecedented and the unique multi-omic datasets will provide many novel insights. The tissue mapping efforts will be supported by commercially available and open-source state-of-the-art 3D reconstruction software to create browsable 3D RNA/protein/PTM/lipid/metabolite maps of the pancreas. Undergirding the tissue characterization and 3D organ map reconstructions efforts will be a robust organ procurement, processing and distribution network. Specifically, we will: (1) Procure, process and distribute samples of normal pancreas from non-diseased donors through a robust procurement, processing, and distribution network. (2) Perform comprehensive high-resolution multi-omics tissue mapping through innovative and complementary platforms for unbiased and targeted analyses (that includes gene and protein expression, and PTM, metabolite and lipid abundances). (3) Establish browsable 3D multi-omics (RNA / protein / PTM / lipid / metabolite)-based maps of normal non-diseased pancreas; and to disseminate methods and tools to the HIVE and other TMCs.