Spatial Recovery of the Hepatic Lobule Using Single Cell RNA Sequencing

Hepatocytes perform different metabolic functions depending on their proximity to the portal triad (periportal) or central vein (perivenous) in the liver lobule. To improve our understanding of the spatial and functional heterogeneity of hepatocytes, we used single cell RNA sequencing (scRNA-seq) and a novel bioinformatics method, Wave-Crest, to reorder hepatocytes along the periportal to perivenous axis. After isolating hepatocytes from an 8-week old male C57BL/6 mouse, performing scRNA-seq, and reordering the cells along the periportal to perivenous axis, Wave-Crest allowed us to identify novel genes differentially expressed along the axis. Using immunocytochemistry, we verified that select novel genes were expressed in the spatial pattern predicted by Wave-Crest. Hence, our study demonstrates a new approach for recovering spatial information from scRNA-seq data. Overall design: Single cell RNA-seq was performed from primary mouse hepatocytes. A total of 149 cells were sequenced.