Human Pluripotent stem cells-derived Inner ear organoids recapitulate otic development in vitro
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ABSTRACT:
PROVIDER: PRJNA953046 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR24099824.fastq.gz | Fastqsanger.gz | |||
| SRR24099825.fastq.gz | Fastqsanger.gz | |||
| SRR24099826.fastq.gz | Fastqsanger.gz | |||
| SRR24099827.fastq.gz | Fastqsanger.gz | |||
| SRR24099828.fastq.gz | Fastqsanger.gz |
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Project description:The molecular characterization of early stages of human inner ear development is limited by the difficulty in accessing samples at early gestational stages. Some aspects of inner ear morphogenesis can be recapitulated using pluripotent stem cell directed differentiation in inner ear organoids (IEOs). Once validated and benchmarked, these models could provide a unique tool to complement and refine our understanding of human otic differentiation and could be used to model developmental defects.Here we provide a first characterization of early human embryonic otocyst development and compare the primary tissue to the iPSC-derived inner ear cell types. Multiplex immunostaining and single cell RNA sequencing were used to characterize human iPSC-derived IEOs at 3 key developmental steps, providing a new and unique signature of in vitro derived otic- placode, epithelium, neuroblasts and sensory epithelia. The expression and localization of key markers were further evaluated in human embryos. We show that the otic placode derived in vitro (day 8-12) matches marker expression of Carnegie Stage (CS) 11 embryos, and subsequently (day 20-40) gives rise to otic epithelia and neuroblasts comparable to the CS13 embryonic stage. Differentiation of sensory epithelia, including supporting cells and hair cells, starts in vitro at day 50-60 of culture. The maturity of these cells is equivalent to vestibular sensory epithelia at week 10 or cochlear tissue at week 12 of development, prior to functional onset. Taken together these data indicates that the current state of the art protocol enables the specification of bona fide otic tissue, supporting further application of IEOs to model inner ear biology and disease
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Project description:Mutations in the chromatin remodeling enzyme CHD7 cause CHARGE syndrome, which affects multiple organs including the inner ear. We investigated how CHD7 mutations affect otic development in human inner ear organoids. We found loss of CHD7 or its chromatin remodeling activity leads to complete absence of hair cells and supporting cells, which can be explained by dysregulation of key otic development-associated genes in mutant otic progenitors. Further analysis of the mutant otic progenitors suggested that CHD7 can regulate otic genes through a chromatin remodeling-independent mechanism. Results from transcriptome profiling of hair cells revealed disruption of deafness gene expression as a potential underlying mechanism of CHARGE-associated sensorineural hearing loss. Notably, co-differentiating CHD7 knockout and wild-type cells in chimeric organoids partially rescued mutant phenotypes by restoring otherwise severely dysregulated otic genes. Taken together, our results suggest that CHD7 plays a critical role in regulating human otic lineage differentiation and deafness gene expression.
2022-07-21 | GSE208585 | GEO
Project description:To investigate pathogenic mechnism of hearing loss in inner ear organoids in PAX3 gene mutation of WS1 patient in vitro , we established the iPSCs line from one WS1 patient carrying a heterozygous mutation in the PAX3 gene and one healthy control. We also constructed the iPSCs line from isogenic CRISPR/Cas9 corrected iPSCs of PAX3 gene mutation. These iPSCs were differentiated into inner ear organoid-like structure with otic vesicles-specific marker.
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Project description:The mechanical properties in the inner ear microenvironment play a key role in its patterning during embryonic development. To recapitulate inner ear development in vitro, three-dimensional tissue engineering strategies including the application of representative tissue models and scaffolds are of increasing interest. Human inner ear organoids are a promising model to recapitulate developmental processes; however the current protocol requires Matrigel that contains ill-defined extracellular matrix components. Here, we implement an alternative, chemically-defined, dynamic hydrogel to support differentiation of human inner ear organoids. Specifically, thiol-norbornene and hydrazide-aldehyde click chemistries are used to fabricate inner ear organoid-laden, gelatin-based scaffolds. We identify optimal formulations to support hair cell development with comparable efficiency and fidelity to Matrigel-cultured organoids. These results suggest that the chemically-defined hydrogel may serve as a viable alternative to Matrigel for inner ear tissue engineering.
2025-01-09 | GSE277377 | GEO
Project description:The morphogenesis of the otic vesicle (OV) to form inner ear organs serves as an excellent model system to understand cell fate acquisition on a single cell level. Tbx2 and Tbx3 (Tbx2/3) encode closely related T-box transcription factors that are expressed widely in the mammalian otic vesicle (OV). Inactivation of both genes in the Pax2-Cre lineage (Tbx2/3cKO) results in failed morphogenesis of the OV into inner ear organs. To understand the basis of these defects, single cell RNA-sequencing (scRNA-seq) was performed on the OV lineage using Pax2-Cre, in controls versus Tbx2/3cKO embryos, at stage E10.5. We identified a multipotent population termed otic progenitors that are localized to the anterior ventrolateral region of the OV in controls and are marked by expression of Fgf18, Sox3, and Cxcl12. The otic progenitor population was increased three-fold in Tbx2/3cKO embryos, concomitant with dysregulation of genes in these cells as well as reduced progression to more differentiated states of prosensory and nonsensory cells. An ectopic neural population of cells was detected in the posterior OV of Tbx2/3cKO embryos due to increased expression of Neurog1 and NeuroD1 but with reduced maturation. As all three cell fates were affected in Tbx2/3cKO embryos, we suggest that Tbx2/3 promotes progression of multipotent otic progenitors to more differentiated cell types in the OV.
2022-12-12 | GSE185172 | GEO
Project description:In 2014, a method was introduced to differentiate mouse embryonic stem cells into inner ear vestibular-like sensory epithelia in vitro. The resulting inner ear organoids represent a potentially inexhaustible source of tissues for investigating mechanosensory hair cell development, function, and responses to ototoxic and regenerative treatments. However, there has been limited exploration into how closely the molecular characteristics of organoid-derived hair cells match those that develop in vivo. To address this gap, we have employed single-cell RNA sequencing (scRNA-seq) to generate a comprehensive atlas of inner ear organoid development at six stages, spanning the formation of definitive ectoderm to the emergence of sensory hair cells. Here, we specifically utilize our inner ear organoid atlas to define the dynamic changes in gene expression that occur during otic vesicle cell maturation into sensory epithelial supporting cells and hair cells.
2024-12-04 | GSE252570 | GEO
Project description:Inner ear organoids recapitulate development and are intended to generate cell types of the otic lineage for applications such as basic science research and cell replacement strategies. Here, we use single-cell sequencing to study the cellular heterogeneity of late-stage mouse inner ear organoid sensory epithelia, which we validated by comparison with data sets of the mouse cochlea and vestibular epithelia. We resolved supporting cell sub-types, cochlear like hair cells, and vestibular Type I and Type II like hair cells. While cochlear like hair cells aligned best with an outer hair cell trajectory, vestibular like hair cells followed developmental trajectories similar to in vivo programs branching into Type II and then Type I extrastriolar hair cells. These results highlight the transcriptional accuracy of the organoid developmental program but will also inform future strategies to improve synaptic connectivity and regional specification.
2024-02-13 | GSE242675 | GEO
Project description:CHD7 regulates otic lineage differentiation and sensory epithelium generation in human inner ear organoids
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Project description:Six1-null mice display developmental defects in the inner ear associated to aberrant senescence. To understand the molecular basis of this phenotype, here we investigated gene expression profiles of otic vesicles from Six1-null and wild-type embryos at developmental stage E10.5.
2023-04-20 | GSE193334 | GEO
Project description:Our molecular understanding of the early stages of human inner ear development has been limited by the difficulty in accessing fetal samples at early gestational stages. As an alternative, previous studies have shown that inner ear morphogenesis can be partially recapitulated using induced pluripotent stem cells directed to differentiate into inner ear organoids (IEOs). Once validated and benchmarked, these systems could represent unique tools to complement and refine our understanding of human otic differentiation and model developmental defects. Here, we provide the first direct comparisons of the early human embryonic otocyst and fetal sensory organs with human IEOs. We use multiplexed immunostaining and single-cell RNA-sequencing to characterize IEOs at three key developmental steps, providing a new and unique signature of in vitro-derived otic placode, epithelium, neuroblasts and sensory epithelia. In parallel, we evaluate the expression and localization of crucial markers at these equivalent stages in human embryos. Together, our data indicate that the current state-of-the-art protocol enables the specification of bona fide otic tissue, supporting the further application of IEOs to inform inner ear biology and disease.
| S-EPMC10565253 | biostudies-literature