Microfluidics Platform for Spatial Multi-Omics Analysis of Tissue at Single Cell Resolution

Project Summary – Abstract AtlasXomics will develop a transformative single-cell resolution multi-omics platform to help researchers and drug developers understand the cell-cell interactions that drive tissue function and disease. With this SBIR application, AtlasXomics will improve upon its existing Deterministic Barcoding in Tissue for spatial omics sequencing (DBiT-seq) which combines microfluidics and next generation sequencing (NGS) to enable researchers to spatially map the cell tissue architecture across the transcriptome (~20,000 genes), epigenome (genome-wide chromatin accessibility and histone modifications) and proteome (hundreds of proteins simultaneously). The platform received significant market interest after its recent publication in Cell in 2020 and its feature in Nature’s 2020 methods of the year. The spatial omics market has seen rapid growth where in 2020 alone, the spatial transcriptomics field has attracted over $100M in venture capital to address a potential market that is estimated to be as large as $10 billion dollars. However, there is still no spatial omics platform that can achieve both single-cell resolution and comprehensive coverage of the multiple omics to truly decipher the cell-to-cell interactions that drive disease. By providing single-cell, multi-omic spatial data to as many researchers as possible, AtlasXomics can help enable a new era of discovery into tissue function and disease. DBiT-seq uniquely utilizes microfluidics to annotate target analytes (mRNA, proteins and/or other biomolecules) in situ (in tissue) with DNA barcodes in a grid of rows and columns, similar to a chessboard, that are then quantified through Next-Generation Sequencing (NGS). The key advantage of this method is that reagents are diffused into tissue, disturbing their biology and spatial configuration as little as possible while creating a high-fidelity molecular image. Our long- term goal is to industrialize this versatile tool from academic proof-of-concept to a robust, affordable, and scalable discovery platform. In Specific Aim 1, we will develop a new prototype device that achieves single cell resolution by refining our existing microfluidic design. In Specific Aim 2, we will use this device to create detailed single cell multi-omics maps (epigenome, transcriptome and proteome) of the mouse embryo. We will then validate our results by comparing them to standard methods, such as single-cell sequencing, immunofluorescence, and single-molecule fluorescence in situ hybridization (smFISH). In Phase II, we plan to scale the platform by improving useability through automation, and by improving performance through expanding the applications of the platform.