Spatiotemporal transcriptomic analyses reveal molecular gradient patterning during development and the tonotopic organization along the cochlear axis

Disruption of cochlear architecture and development can lead to malfunction, resulting in hearing defects. However, the spatial molecular profiles critical for hearing function remain poorly understood due to the structural complexity of the cochlea. In this study, we performed comprehensive spatiotemporal transcriptomic analyses on the developing and adult cochlea, identifying numerous genes with gradient expression patterns in hair cells (HCs) and spiral ganglion neurons (SGNs) across the apical-to-basal axis. The gradient gene Myo7a , a well-known HC marker, established a decreasing gradient in outer hair cells (OHCs) from the apical to basal regions in adulthood. In contrast, the other class of gradient genes exhibited an opposing expression pattern to Myo7a along the cochlear axis in adulthood, such as Calb2 in HCs and Nefh in SGNs, which potentially corresponds to the cochlear tuning properties for sensing gradient frequency sounds. Importantly, our analyses provided compelling evidences for the existence of distinct spatial subtypes of OHCs. The spatial analyses revealed regional heterogeneity in cell communication intensity between HCs and SGNs, with the weakest intensity at the apex, potentially aligning this region for detection of low-frequency sound. This study systematically characterized the fine spatial organizations in HCs, SGNs, and their regionalized cell-communications within the cochlea, offering insights into the morphological and molecular foundations underlying cochlear tonotopic organization and frequency discrimination.