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

项目摘要-摘要 Xomics将开发一个变革性的单细胞分辨率多组学平台， 研究人员和药物开发人员了解驱动组织功能的细胞-细胞相互作用 和疾病有了这个SBIR应用程序，Xomics将改进其现有的确定性 用于空间组学测序的组织中的条形码（DBiT-seq），其结合了微流体和 下一代测序（NGS），使研究人员能够空间映射细胞组织 转录组（约20，000个基因）、表观基因组（全基因组染色质） 可及性和组蛋白修饰）和蛋白质组（同时包含数百种蛋白质）。的 该平台最近于2020年在Cell上发表， 《自然》杂志2020年年度方法中的一个特色。 空间组学市场增长迅速，仅在2020年， 该领域吸引了超过1亿美元的风险投资，以解决一个潜在的市场，估计 达到100亿美元。然而，仍然没有空间组学平台可以 实现单细胞分辨率和多组学的全面覆盖， 解读导致疾病的细胞间相互作用。通过提供单细胞、多组学空间 数据尽可能多的研究人员，Xomics可以帮助实现一个新的发现时代 组织功能和疾病。 DBiT-seq独特地利用微流体来注释靶分析物（mRNA、蛋白质和/或其他靶分析物）。 生物分子）原位（在组织中）与行和列网格中的DNA条形码，类似于 棋盘，然后通过下一代测序（NGS）进行量化。关键 这种方法的优点是试剂扩散到组织中，干扰它们的生物学， 空间构型尽可能少，同时创建高保真分子图像。我们长久以来- 长期目标是将这种多功能工具从学术概念验证工业化， 经济实惠且可扩展的发现平台。 在具体目标1中，我们将开发一种新的原型设备，通过以下方式实现单细胞分辨率： 改进我们现有的微流体设计。在具体目标2中，我们将使用此设备创建详细的 小鼠胚胎的单细胞多组学图谱（表观基因组、转录组和蛋白质组）。我们 然后将通过将其与标准方法（如单细胞）进行比较来验证我们的结果 测序、免疫荧光和单分子荧光原位杂交 （smFISH）。在第二阶段，我们计划通过自动化提高可用性来扩展平台， 以及通过扩展平台的应用来提高性能。

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.