Human brain organoids assemble functionally integrated bilateral optic vesicles
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ABSTRACT:
PROVIDER: PRJNA743802 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR15042265_1.fastq.gz | Fastqsanger.gz | |||
| SRR15042265_2.fastq.gz | Fastqsanger.gz | |||
| SRR15042266_1.fastq.gz | Fastqsanger.gz | |||
| SRR15042266_2.fastq.gz | Fastqsanger.gz | |||
| SRR15042267_1.fastq.gz | Fastqsanger.gz |
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Project description:During embryogenesis, optic vesicles develop from the diencephalon via a complex process of organogenesis. Using iPSC-derived human brain organoids, we attempted to simplify the complexities and demonstrate the formation of forebrain-associated bilateral optic vesicles, cellular diversity, and functionality. Around day thirty, brain organoids could assemble optic vesicles, which progressively develop as visible structures within sixty days. These optic vesicle-containing brain organoids (OVB-Organoids) constitute a developing optic vesicle’s cellular components, including the primitive cornea and lens-like cells, developing photoreceptors, retinal pigment epithelia, axon-like projections, and electrically active neuronal networks. Besides, OVB-Organoids also display synapsin-1, CTIP-positive, myelinated cortical neurons, and microglia. Interestingly, various light intensities could trigger photoreceptor activity of OVB-Organoids, and light sensitivities could be reset after a transient photo bleach blinding. Thus, brain organoids have the intrinsic ability to self-organize forebrain-associated primitive sensory structures in a topographically restricted manner and can allow conducting interorgan interaction studies within a single organoid.
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Project description:Human pluripotent stem cells (PSCs) represent an exciting tool to investigate the mechanisms of human eye development and to build models of human retinal disease. When grown in 3D, these cells can self-organize into laminar organized retinas; however, significant variation in the size, shape and composition of individual organoids exists, and this variation can create challenges. Neither the microenvironment nor the timing of critical growth factors driving eye formation or retinogenesis are fully understood. To explore the dynamics of early retinal organoid development, we have developed a SIX6-GFP reporter line that enables the systematic optimization of early eye field development, allowing for the identification of conditions that favor optic development. We found that SIX6 expression in 3D optic structures is influenced by small molecules regulating SHH and WNT signaling in a dose and time dependent fashion. In addition, we demonstrated that hypoxic growth conditions favor SIX6 expression, and promote eye formation. The systematic optimization of these pathways leads to optic vesicles with robust SIX6 expression and global gene expression profiles consistent with a retinal identity. The use of stem cell derived human retinal organoids with a real time marker for retinogenesis, therefore, represents an important model for probing the mechanisms of early human eye development.
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Project description:The optic vesicle in the developing embryonic eye contains a multitude of neuroepithelial progenitors that subsequently differentiate into functionally distinct domains of the optic cup, such as the neural retina, pigment epithelium, and optic stalk. To investigate cell-type diversity across early optic vesicles before regionalization of the optic cup, we performed single-cell RNA-sequencing (scRNA-seq) using 7,989 cells from the presumptive eye area in mouse embryos at the 12–26-somite stages at five developmental time points. We demonstrated the presence of seven optic vesicle populations, including three unique cell types located in the ventricular surface or dorsoventral areas of the optic vesicle structure. Moreover, the remaining four populations of retinal progenitor cells could be classified according to their stage-dependent time point, and these cells exhibited altered expression of several structural and metabolic key genes, such as Col9a1 and Ckb, just before regionalization of the optic cup. From these data, we provide the first report on stage-dependent transcriptional profiles during initial retinal specification at single-cell resolution and highlight the unexpected developmental heterogeneity of the murine optic vesicle structure.
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Project description:To identify genes regulated by Rx3 during optic vesicle morphogenesis, adult zebrafish carriers of a null rx3 mutation were mated. Before 13 hours post fertilization (hpf), the earliest time point at which optic vesicle evagination phenotypes could be reliably detected, offspring were phenotypically separated into pools comprising of mutants with an absence of optic vesicles or siblings exhibiting a wild-type phenotype. Three replicates of pooled RNA samples from 13 hpf eyeless mutants (rx3-/-) or phenotypically wild-type siblings (rx3+/+ or rx3+/-), and one replicate of 13 hpf wild-type zebrafish larva were collected for whole transcriptome sequencing. Whole transcriptome sequencing (RNA-seq) was performed on zebrafish rx3-/- mutants, wild-type siblings and wild-type AB strains at 13 hpf
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Project description:SIX6 regulation in human optic vesicles is mediated by early microenvironmenta factors
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Project description:To identify genes regulated by Rx3 during optic vesicle morphogenesis, adult zebrafish carriers of a null rx3 mutation were mated. Before 13 hours post fertilization (hpf), the earliest time point at which optic vesicle evagination phenotypes could be reliably detected, offspring were phenotypically separated into pools comprising of mutants with an absence of optic vesicles or siblings exhibiting a wild-type phenotype. Three replicates of pooled RNA samples from 13 hpf eyeless mutants (rx3-/-) or phenotypically wild-type siblings (rx3+/+ or rx3+/-), and one replicate of 13 hpf wild-type zebrafish larva were collected for whole transcriptome sequencing.
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Project description:We investigate the therapeutic effect of mesenchymal stem cell-derived small extracellular vesicles (MSC-sEVs), a potent immune-modulating therapy for tissue regeneration, in repairing optic nerve damage. Intraocular administration of MSC-sEVs promotes both RGC survival and axon regeneration against optic nerve crush injury. Mechanistically, MSC-sEVs recruits a neural restorative population of hematogenous Ly6Clow monocyte/monocyte-derived macrophage (Mo/MΦ). Gain-of-function by intravitreal administration of the donor Ly6Clow Mo/MΦ markedly improves neurological outcomes in vivo. We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 different cells at two time points.
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Project description:Reactive gliosis is a complex process that involves profound changes in gene expression. We used microarray to indentify differentially expressed genes and to investigate the molecular mechanisms of reactive gliosis in optic nerve head in response to optic nerve crush injury. C57Bl/6 female mice were 6-8 weeks old at the time of optic nerve crush surgery. The optic nerve in the left eye was crush 1 mm behind the globe for 10 seconds and the right eye served as contralateral control. The animals were allowed to recover for 1 day, 3 day, 1 week, 3 weeks and 3 months before the optic nerve heads were collected. The naive control mice did not receive any surgery in either eye. Due to the small tissue size of the mouse optic nerve head, two optic nerve heads were pooled together for each microarray chip. The left eyes and the right eyes of two mice were combined respectively to form one pair of experiment and control samples. There were five biological replicates (10 mice) for each condition.
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Project description:A major risk factor for glaucomatous optic neuropathy is the level of intraocular pressure (IOP), which can lead to retinal ganglion cell axon injury and cell death. The optic nerve has a rostral unmyelinated portion at the optic nerve head followed by a caudal myelinated region. The unmyelinated region is differentially susceptible to IOP-induced damage in rodent models and in human glaucoma. While several studies have analyzed gene expression changes in the mouse optic nerve following optic nerve injury, few were designed to consider the regional gene expression differences that exist between these distinct areas. We performed bulk RNA-sequencing on the retina and on separately micro-dissected unmyelinated and myelinated optic nerve regions from naïve C57BL/6 mice, mice after optic nerve crush, and mice with microbead-induced experimental glaucoma (total = 36). Gene expression patterns in the naïve unmyelinated optic nerve showed significant enrichment of the Wnt, Hippo, PI3K-Akt, and transforming growth factor β pathways, as well as extracellular matrix–receptor and cell membrane signaling pathways, compared to the myelinated optic nerve and retina. Gene expression changes induced by both injuries were more extensive in the myelinated optic nerve than the unmyelinated region, and greater after nerve crush than glaucoma. Changes present three and fourteen days after injury largely subsided by six weeks. Gene markers of reactive astrocytes did not consistently differ between injury states. Overall, the transcriptomic phenotype of the mouse unmyelinated optic nerve was significantly different from immediately adjacent tissues, likely dominated by expression in astrocytes, whose junctional complexes are inherently important in responding to IOP elevation.
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