3D reconstruction of the mouse cochlea from scRNA-seq data suggests morphogen-based principles in apex-to-base specification

In the mammalian auditory system, frequency discrimination depends on numerous morphological and physiological properties of the organ of Corti, which gradually change along the apex-to-base (tonotopic) axis of the organ. For example, the basilar membrane stiffness changes tonotopically, thus affecting the tuning properties of individual hair cells. At the molecular level, those frequency-specific characteristics are mirrored by gene expression gradients; however, the molecular mechanisms controlling tonotopic gene expression in the mouse cochlea remain elusive. Through analyzing single-cell RNA sequencing (scRNA-seq) data from E12.5 and E14.5 time points, we predicted that morphogens, rather than a cell division-associated mechanism, confer spatial identity in the extending cochlea. Subsequently, we reconstructed the developing cochlea in 3D space from scRNA-seq data to investigate the molecular pathways mediating positional information. The retinoic acid (RA) and hedgehog pathways were found to form opposing apex-to-base gradients, and functional interrogation using mouse cochlear explants suggested that both pathways jointly specify the longitudinal axis. [Display omitted] •3D reconstruction of the developing cochlear duct from scRNA-seq data•Morphogens, not cell cycle exit, confer tonotopic information in the cochlea•Opposing RA and SHH gradients control apex-to-base gene expression in the cochlea Wang and Chakraborty et al. demonstrate that morphogens rather than a timing-related mechanism mediate positional information along the apex-to-base axis of the murine cochlea. Moreover, two morphogens, retinoic acid and sonic hedgehog, were identified to form opposing morphogen gradients, thereby controlling spatial gene expression along the apex-to-base axis.