The single-cell transcriptional landscape of neuronal fates in the developing mouse cochlea

The spiral ganglion neurons (SGNs) of the cochlea are essential for auditory perception by transmitting complex auditory information from hair cells (HCs) to the brain, yet the molecular mechanisms generating their diversity are unknown. Here we used single cell RNA sequencing to reconstruct the developmental trajectories of SGN cell fates and identified genes and gene regulatory networks that participate to changes in developmental competence and cell states, and in specification of each major cell types. Our analysis also identified gene modules associated with the sequential binary decisions that delineate neuron fate choices along the diversification tree. Transcriptome analysis of both developing SGN and HC types further revealed cell-state specific cell-cell signaling potentially playing a role in the differentiation and connectivity profile of SGNs as well as human deafness-associated genes, both previously known and novel. Overall, our results identify molecular principles that shape SGN differentiation and will facilitate further studies of SGNs development, physiology and dysfunction. Overall design: Smart-Seq2 protocol was performed on single isolated cells by Eukaryotic Single Cell Genomics Facility at SciLifeLab, Stockholm. From the Ntrk3Cre;R26tdTOM E14.5 samples, we isolated a total of 135 cells, including 82 neurons and 53 OM. From the PVcre;R26tdTOM mice we isolated a total of 2139 cells: 229 at E15.5 (161 neurons and 68 OM), 661 at E16.5 (580 neurons and 73 OM and 8 HCs), 72 at E17.5 (71 neurons and 1 HC) and 667 at E18.5 (611 neurons and 66 HC). The P3 the transcriptional data was obtained from our previous study.