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Resolving fate bifurcation of photoreceptor precursor in human retinal organoid by single-cell transcriptomics

ABSTRACT: Resolving fate bifurcation of photoreceptor precursor in human retinal organoid by single-cell transcriptomics

PROVIDER: PRJNA753130 | ENA |

REPOSITORIES: ENA

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Resolving fate bifurcation of photoreceptor precursor in human retinal organoid by single-cell transcriptomics

Project description:Cone and rod photoreceptors in human enable daytime color and nighttime dark vision respectively and abnormality in photoreceptor development results in blindness. However, when and how the two photoreceptors are fate-determined during development is largely unknown. Herein, we established a cell atlas for human photoreceptor development, based on single-cell transcriptomic profiling of engineered human retinal organoids engineered to trace the photoreceptor lineages during developmentto monitor the photoreceptor lineages during development. For the first time, we demonstrated the subtypes of photoreceptor precursors based on unsupervised clustering of single-cell transcriptomesbifurcation of cell fate in the photoreceptor precursors, withwith the conespecific expression of molecular marker gene PDE6H ands for cone precursor and rod marker gene NR2E3 differentially expressed among others precursor. Further dissection of transcriptional segregation of the two precursors uncovered PHLDA1 as an intrinsic regulator intrinsic regulator in the fate bifurcation of of the rod-related gene networksphotoreceptor subtypes. Photoreceptor precursors with decreased PHLDA1 yield more cones while reduced the number of rods. The PHLDA1-mediated modification of cell fate can be directed downstream of IGF1 signaling, and exhibited an inhibitory effect on AKT phosphorylation which was associated with cone differentiation., which directed the downstream effects of IGF1 to promote the rod differentiation. Collectively, our data identified PHLDA1 as a novel regulator of fate determination of photoreceptors at the precursor stage, andour study shed lights on the cellular and molecular mechanisms of human photoreceptor precursor specification, and provided a framework to study mechanisms of cell fate determination of human retinal cells.

2023-09-14 | GSE181737 | GEO

Dynamic redistribution of CTCF demarcates bifurcation of cytotoxic effector and memory precursor programs

Project description:Dynamic redistribution of CTCF demarcates bifurcation of cytotoxic effector and memory precursor programs

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Dynamic redistribution of CTCF demarcates bifurcation of cytotoxic effector and memory precursor programs [Cut & Run]

Project description:Dynamic redistribution of CTCF demarcates bifurcation of cytotoxic effector and memory precursor programs [Cut & Run]

| PRJNA858437 | ENA

Dynamic redistribution of CTCF demarcates bifurcation of cytotoxic effector and memory precursor programs [ATAC-Seq]

Project description:Dynamic redistribution of CTCF demarcates bifurcation of cytotoxic effector and memory precursor programs [ATAC-Seq]

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Dynamic redistribution of CTCF demarcates bifurcation of cytotoxic effector and memory precursor programs [RNA-Seq]

Project description:Dynamic redistribution of CTCF demarcates bifurcation of cytotoxic effector and memory precursor programs [RNA-Seq]

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Dynamic redistribution of CTCF demarcates bifurcation of cytotoxic effector and memory precursor programs [Hi-C]

Project description:Dynamic redistribution of CTCF demarcates bifurcation of cytotoxic effector and memory precursor programs [Hi-C]

| PRJNA910134 | ENA

Effective transplantation of photoreceptor precursor cells selected via cell surface antigen expression.

Project description:Microarray analysis of postnatal NrlGFP-expressing rod photoreceptor precursors. NrlGFP positive versus NrlGFP negative at postnatal day 4

2013-06-07 | E-MEXP-3922 | biostudies-arrayexpress

NR2E3 loss disrupts photoreceptor cell maturation and fate in human organoid models of retinal development

Project description:While dysfunction and/or death of light-detecting photoreceptor cells underlies most inherited retinal dystrophies, knowledge of the species-specific details of human rod and cone photoreceptor cell development remains limited. Here, we generate retinal organoids using induced pluripotent stem cells (iPSC) derived from a patient with genetic photoreceptor disease, an isogenic control, and an unrelated control. Organoids were sampled using single-cell RNA sequencing across the developmental window encompassing photoreceptor specification, emergence, and maturation; up to 260 days of in vitro differentiation. Using single-cell transcriptomics data, we reconstruct the rod photoreceptor developmental lineage and identify a branchpoint in development unique to the disease state that gives rise to a divergent rod photoreceptor cell population. We show that the rod-specific transcription factor NR2E3 is required for the proper expression of genes involved in phototransduction, including expression of the light-sensitive protein rhodopsin, which is absent in divergent rods. NR2E3-null rods additionally misexpress several cone-specific phototransduction genes at both the transcript and protein level. Using joint multimodal single-cell sequencing on late-stage retinal organoids, we further identify the specific putative regulatory sites where rod-specific factors act to steer rod and cone photoreceptor cell development. Importantly, these findings are strikingly different than that observed in rodent models of disease. Together, these data provide a roadmap of human photoreceptor development and leverage patient iPSCs to define the specific roles of rod transcription factors in photoreceptor cell emergence and maturation.

2024-04-01 | GSE236197 | GEO

Dynamic redistribution of CTCF demarcates bifurcation of cytotoxic effector and memory precursor programs [CUT&Run 3]

Project description:Dynamic redistribution of CTCF demarcates bifurcation of cytotoxic effector and memory precursor programs [CUT&Run 3]

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Dynamic redistribution of CTCF demarcates bifurcation of cytotoxic effector and memory precursor programs [CUT&Run 2]

Project description:Dynamic redistribution of CTCF demarcates bifurcation of cytotoxic effector and memory precursor programs [CUT&Run 2]

| PRJNA910136 | ENA