Derivation of cochlear organoids from human pluripotent stem cells reveals tight transcriptome-structure coupling during organogenesis

A balance of morphogen gradients during embryogenesis is thought to determine the identity of inner ear end organs. We applied this developmental principle to aggregates of human pluripotent stem cells and found that modulations of Sonic Hedgehog and WNT signaling promote stem cell-derived otic progenitors to express ventral otic markers. Strikingly, these ventralized otic progenitors gave rise to hair cells with short hair bundles comprised of stereocilia arrayed in a geometry reminiscent of cochlear hair cells. Moreover, these ventralized hair cells expressed multiple markers defining outer or inner hair cells in the cochlea. These results reveal that early morphogenic signals are sufficient for not only establishing cochlear gene expression, but also defining structural properties pertaining to the cochlear sensory epithelium. Aggregates of hESCs were subject to 3 different culture conditions to induce otic tissue and hair cell development. 10X Chromium v3' v3 was used to sequence dissociated aggregates at three time points: day 20, day 80, and day 109. Three conditions were examined at day 20, and two conditions were examined at both day 80 and 109.