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Time-Series Single Cell RNA Sequencing of Inner Ear Organoid Development

ABSTRACT: We report the application of single cell RNA sequencing for determining cell type and quantity in developing inner ear organoids derived from human pluripotent stem cells. By obtaining samples from multiple time points throughout differentiation, we developed a roadmap at single cell resolution of the multiple cell lineages which give rise to in vitro inner ear tissue as well as 'off-target' tissue types. We find that the cells in the day 0 sample contained primarily a homogenous population of pluripotent stem cells. On day 3, after treatment with BMP4, we find that the cells have differentiated into a split between surface ectoderm, the progenitor of the inner ear tissue, and neuroectoderm. On day 6 and 8, we observed the emergence of cranial placode tissue, both anterior and posterior. Then, after treatment starting on day 8 with a WNT agonist, CHIR, we observed the maturation of inner ear tissue into hair cells and neurons, starting on day 18 and increasing through the last time point collected, day 36. This study provides an atlas of inner ear organoid differentiation from human pluripotent stem cells.

ORGANISM(S): Homo sapiens

PROVIDER: GSE188936 | GEO | 2021/11/23

REPOSITORIES: GEO

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Project description:The inner ear in mammals is derived from a simple ectodermal thickening called the otic placode. Through a series of complex morphological changes, the placode forms the mature inner ear comprising of the auditory organ (cochlea) and the vestibular/balance organs (utricle, saccule, and three semi-circular canals). The vast majority of genes known to be involved during inner ear development have been found through mutational screens or by chance. To identify genes that can serve as novel candidates required for inner ear development, and also candidate genes for uncloned human deafnesses, inner ear tissues from mouse embryos from E9 to E15 were microdissected and expression-profiled at half-day intervals. Also profiled was the non-inner ear mesenchymal tissue surrounding the inner ear tissue. Various patterns of gene expression were identified, and significant biological pathways that these genes represented were identified. Also identified were mouse genes whose human orthologs are located within uncloned non-syndromic deafness intervals, thus serving as candidates for sequence analysis. Experiment Overall Design: Inner ear tissues from E9 to E15 were microdissected at half-day intervals. E9 is the earliest stage when the otic placode is clearly visible and able to be microdissected cleanly. E15 is the stage when all the organs of the inner ear have become established, as have the sensory hair and non-sensory support cells within those organs. For each of the stages from E9 to E10, whole inner ears were profiled. For each of the stages from E10.5 to E12, the primordial cochlear and vestibular organs were profiled separately. For each of the stages from E12.5 to E15, the cochlea and the saccule were profiled separately, whereas the utricle and the three ampullae were combined and profiled together. Any given tissue from any given stage was a collection of anywhere between 4 to 17 identical tissues, and was obtained in duplicate (i.e. from different litters). Hence, a total of 58 inner ear samples were obtained. Moreover, non-inner ear tissue found in the immediate vicinity of inner ear tissue was also obtained and profiled. Specifically, all non-inner ear tissue from E9 was profiled in duplicate. Non-inner ear tissue from E9.5 to E10.5 was pooled and profiled together (in duplicate), whereas that from E11 to E15 was pooled and profiled together (also in duplicate). Therefore, a total of 6 non-inner samples were obtained.