Abstract P1185: Spatial Transcriptome Profiling In The Mouse Heart With Single-Cell Resolution

Abstract

Background: The spatial organization of the diverse cells in the heart shapes biological function. For instance, during the inflammatory and fibrotic processes that are central to heart disease, many cells act mainly within their local microenvironment. Recent studies using single-cell RNA sequencing (scRNA-seq) have provided a detailed list of the cell types and states involved in development, homeostasis and in cardiovascular diseases. However, scRNA-seq requires tissue dissociation, which removes spatial information and thereby limits our ability to determine how cells interact with each other to maintain health or cause disease. As a consequence, the precise spatial organization of cell types and states in the mammalian heart remains unknown. We sought to address this knowledge gap by using multiplexed error-robust fluorescence in situ hybridization (MERFISH), a method that enables simultaneous identification and localization of single transcripts from hundreds of different genes in intact tissue sections. Methods/Results: We adapted MERFISH and developed a new single-cell image segmentation method to creating a single-cell atlas of the mouse heart. First, we designed and constructed a 128-gene MERFISH probe library including cell type marker genes and also genes covering a broad range of cardiac signaling pathways. We then optimized sample preparation, including cell boundary staining and tissue clearing. Once optimized, we used this approach to image 10 μm-thick sections from healthy mouse heart, resolving tens of thousands of cells and millions of transcripts. Our data thus constitute the first single-cell spatial transcriptome atlas of the mouse heart. Conclusion: Through our newly developed cardiac MERFISH platform, we identified tens of thousands of cells and labeled millions of individual RNA transcripts in intact sections of mouse heart. Our cellular transcriptome profile maps enable new insights into how the organization of the heart shapes its biological function.