SBIR Abstract Single cell biology is a multi-disciplinary study to investigate how large numbers of molecular species interact with each other in single cells, and how large population of cells work together as complex systems. Cells within a given tissue, even when they are morphologically similar, are heterogeneous in their gene expression patterns. Defining gene expression patterns at the single-cell level within the context of the normal tissue architecture is essential to understanding tissue function and development, and will ultimately benefit precision and personalized medicine. However, current tools for single-cell gene expression analysis, such as single-cell RNA sequencing, lack spatial information and have low cell and RNA detection efficiency. Hence, there is an urgent need for better tools for profiling single-cell gene expression patterns in situ ?i.e., within the context of normal tissue architecture and cell-cell relationships. Rainbow UltraFISH is a technology that integrates spatial and sequence information together for single-cell RNA analysis. It uses rapid sequential fluorescent in situ hybridization (FISH) to achieve multiplex RNA detection at high detection efficiency and single- cell resolution. In cultured cell lines, UltraFISH has been shown to complete each round of probe-target hybridization in <10 min, with a detection efficiency of ~90%. In this proposal, we will expand the UltraFISH technology into primary mouse tissue samples, including fresh-frozen tissue (Aim 1), formaldehyde-fixed, frozen tissue (Aim 2), and formalin-fixed, paraffin-embedded tissue (Aim 3). With the successful outcome of this proposal, UltraFISH will be the simplest and fastest technology for single-cell gene expression analysis in situ and ultimately enable more precision medicine.
Project Narrative: Rainbow UltraFISH is a technology that will enable researchers to analyze the expression patterns of hundreds to thousands of genes within single cells in the context of their normal tissue environment. With the coming of the spatial genomics era, UltraFISH will become an essential research tool for a very broad range of biologists and medical scientists in both academia and the biotech industry. It will help answer fundamental questions in all aspects of biology, as well as serve as a powerful tool to unravel the secrets of human disease.