The spinal cord is responsible for transmitting signals from the central nervous system to the muscles and organs throughout the body. It coordinates both autonomic and skeletal movement by innervating unique targets. There are various conditions (such as amyotrophic lateral sclerosis (ALS), spinal muscular atrophy (SMA), and other neuromuscular disorders) that have been associated with spinal cord dysfunction. The spinal cord cell types have well-established morphological, physiological, and functional clusters. On the other hand, single-cell RNA sequencing has defined the cell types via gene markers. Although there might not always be a direct overlap between the structural and transcriptional information, studying these factors together allows a deeper understanding of the spinal cord cell types. The spatial analysis of transcriptomics allows us to investigate the gene expressions while preserving information about the location. STARmap (Spatially-resolved Transcript Amplicon Readout mapping) is a technique that utilizes in-situ RNA sequencing via enzymatic amplification and hydrogel chemistry for the quantitative study of gene expressions. The DNA amplicons are modified with N-hydroxysuccinimide moiety and then copolymerized with acrylamide to create an in-situ hydrogel that allows for an optically transparent structure for sequencing. Using STARmap, we analyzed 1022 genes in the mouse spinal cord. We studied transcriptional heterogeneity in spinal cord cells while preserving its spatial location. The three-dimensional analysis allows us to correlate transcription information with morphology, location, and cell-cell communication. STARmap can be used as a tool to further enhance our knowledge on the relationship of gene expression with location, cellular basis of motor function, and neuromuscular degenerative diseases.

Three dimensional intact tissue transcriptional analysis of mouse spinal cord

ACS Spring 2022

The official archive and repository for all ACS Meetings & Expositions abstracts and select posters or presentations.