Transcriptomic profiling of adult zebrafish photoreceptors
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ABSTRACT:
ORGANISM(S): Danio rerio
PROVIDER: GSE188560 | GEO | 2022/11/10
REPOSITORIES: GEO
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Project description:Vertebrate vision is mediated by two kinds of photoreceptors, rods and cones, responsible for dim- and bright-light vision, respectively. Gene expression differences among cone subtypes remain poorly understood compared with rods. We generated single-cell transcriptome data using a droplet-based approach to reveal the extent of gene expression diversity among adult zebrafish photoreceptor subtypes. Populations of photoreceptor cells were enriched by using the transgenic zebrafish lines, Tg(rho:EGFP)ja2Tg and Tg(gnat2:EGFP)ja23Tg, which express GFP in rods and all cone subtypes, respectively. By analyzing the single-cell transcriptomes, we found that in addition to the four canonical zebrafish cone types (ultraviolet, blue, green and red), there exist subpopulations of green and red cones in the ventral retina that express red-shifted opsin paralogs (opn1mw4 and opn1lw1). This work lays a foundation for future studies aimed at understanding how molecular differences among cone subtypes affect photoreceptor function.
2021-08-30 | GSE175929 | GEO
Project description:Cell type specific gene expression profiling was performed with adult Drosophila photoreceptors. Two genotypes were compared: ninaE wild type control and ninaEG69D/+ mutants that have chronic endoplasmic reticulum stress. To specifically isolate RNAs from these cell types, we drove nuclear envelope-localized EGFP::Msp300KASH expression with the photoreceptor specific Rh1-Gal4 driver. Anti-GFP beads were used to isolate the nuclei from those adult fly photoreceptor cells. Novaseq was used to perform RNA-seq.
2021-10-02 | GSE185134 | GEO
Project description:Investigating neuronal and photoreceptor regeneration in the retina of zebrafish has begun to yield insights into both the cellular and molecular means by which this lower vertebrate is able to repair its central nervous system. However, knowledge about the signaling molecules in the local microenvironment of a retinal injury and the transcriptional events they activate during neuronal death and regeneration is still lacking. To identify genes involved in photoreceptor regeneration, we combined light-induced photoreceptor lesions, laser-capture microdissection (LCM) of the outer nuclear layer (ONL) and analysis of gene expression to characterize transcriptional changes for cells in the ONL as photoreceptors die and are regenerated. Using this approach, we were able to characterize aspects of the molecular signature of injured and dying photoreceptors, cone photoreceptor progenitors and microglia within the ONL. We validated changes in gene expression and characterized the cellular expression for three novel, extracellular signaling molecules that we hypothesize are involved in regulating regenerative events in the retina. Experiment Overall Design: As a means to identify genes necessary for photoreceptor regeneration, we evaluated transcriptional changes for cells in the outer nuclear layer (ONL) as photoreceptors die and are regenerated. To accomplish this, we combined light-induced photoreceptor lesions, laser-capture microdissection (LCM) of the ONL and analysis of gene expression using oligonucleotide arrays.
2008-10-26 | E-GEOD-13068 | biostudies-arrayexpress
Project description:Vertebrate ancestors had only cone-like photoreceptors. The duplex retina evolved in jawless vertebrates with the advent of highly photosensitive rod-like photoreceptors. Despite cones being the arbiters of high-resolution color vision, rods emerged as the dominant photoreceptor in mammals during a nocturnal phase early in their evolution. We investigated the evolutionary and developmental origins of rods in two divergent vertebrate retinae. In mice, we discovered genetic and epigenetic vestiges of short wavelength cones in developing rods and cell lineage tracing validated the genesis of rods from S-cones. Curiously, rods did not derive from S-cones in zebrafish. Our study illuminates several questions regarding the evolution of duplex retina and supports the hypothesis that, in mammals, the S-cone lineage was recruited via the Maf-family transcription factor NRL to augment rod photoreceptors. We propose that this developmental mechanism allowed the adaptive exploitation of scotopic niches during the nocturnal bottleneck early in mammalian evolution.
2016-06-21 | GSE81953 | GEO
Project description:Vertebrate ancestors had only cone-like photoreceptors. The duplex retina evolved in jawless vertebrates with the advent of highly photosensitive rod-like photoreceptors. Despite cones being the arbiters of high-resolution color vision, rods emerged as the dominant photoreceptor in mammals during a nocturnal phase early in their evolution. We investigated the evolutionary and developmental origins of rods in two divergent vertebrate retinae. In mice, we discovered genetic and epigenetic vestiges of short wavelength cones in developing rods and cell lineage tracing validated the genesis of rods from S-cones. Curiously, rods did not derive from S-cones in zebrafish. Our study illuminates several questions regarding the evolution of duplex retina and supports the hypothesis that, in mammals, the S-cone lineage was recruited via the Maf-family transcription factor NRL to augment rod photoreceptors. We propose that this developmental mechanism allowed the adaptive exploitation of scotopic niches during the nocturnal bottleneck early in mammalian evolution.
2016-06-21 | GSE81099 | GEO
Project description:Vertebrate ancestors had only cone-like photoreceptors. The duplex retina evolved in jawless vertebrates with the advent of highly photosensitive rod-like photoreceptors. Despite cones being the arbiters of high-resolution color vision, rods emerged as the dominant photoreceptor in mammals during a nocturnal phase early in their evolution. We investigated the evolutionary and developmental origins of rods in two divergent vertebrate retinae. In mice, we discovered genetic and epigenetic vestiges of short wavelength cones in developing rods and cell lineage tracing validated the genesis of rods from S-cones. Curiously, rods did not derive from S-cones in zebrafish. Our study illuminates several questions regarding the evolution of duplex retina and supports the hypothesis that, in mammals, the S-cone lineage was recruited via the Maf-family transcription factor NRL to augment rod photoreceptors. We propose that this developmental mechanism allowed the adaptive exploitation of scotopic niches during the nocturnal bottleneck early in mammalian evolution.
2016-06-21 | GSE74660 | GEO
Project description:Purpose: Avian photoreceptors are a diverse class of neurons, comprised of four single cones, the two members of the double cone, and rods. Many distinctive features of photoreceptor subtypes, including spectral tuning, oil droplet size and pigmentation, synaptic targets and spatial patterning, have been well characterized, but the molecular mechanisms underlying these attributes have not been explored. Furthermore, the signaling events and transcriptional regulators driving the differentiation of these diverse photoreceptors are currently unknown. Methods: To identify genes specifically expressed in distinct chicken (Gallus gallus) photoreceptor subtypes, we developed fluorescent reporters that label photoreceptor subpopulations, isolated these subpopulations using fluorescence-activated cell sorting, subjected them to next-generation sequencing, and conducted differential expression analysis. Results: We identified hundreds of differentially expressed genes from photoreceptor subpopulations labeled with rhodopsin, red opsin, green opsin, and violet opsin reporters. These genes are involved in a variety of processes, including phototransduction, transcriptional regulation, cell adhesion, maintenance of intra- and extra-cellular structure, and metabolism. Of particular note are a variety of differentially expressed transcription factors, which may drive and maintain photoreceptor diversity, and cell adhesion molecules that may mediate spatial patterning of photoreceptors and act to establish retinal circuitry. Conclusions: These analyses provide a framework for future studies that will dissect the role of these various factors in the differentiation of avian photoreceptor subtypes. mRNA expression profiling of 5 pairs of photoreceptor subtypes isolated from chicken retinal explants, 3 replicates per sample
2014-09-01 | E-GEOD-59850 | biostudies-arrayexpress
Project description:Purpose: The purpose of this study was to identify transcripts of rod photoreceptors of the zebrafish, an important animal model for vision science. Methods: Zebrafish rods, and non-rod retinal cells of the XOPS:eGFP transgenic line, were separated by cell dissociation and fluorescence-activated cell sorting (FACS), followed by RNA-seq. Validation studies used qPCR and in situ hybridization. Some transcripts were examined in sorted retinal cell populations of larval and juvenile retinas and regenerated adult retinas, and in a zebrafish model for rod degeneration. Results: At a false discovery rate of <0.01, 597 transcripts were upregulated in rods vs. non-rod retinal cells, and 1032 were downregulated. 13,324 total transcripts were detected in rods, including many not previously known to be expressed by rods. Transcripts enriched in rods from adult retinas were also enriched in rods from larval and juvenile retinas, and were also enriched in regenerated rods. Many transcripts enriched in rods were upregulated in retinas of wildtype retinas vs. those of a zebrafish model for rod degeneration. Conclusions: We report the generation of an RNA-seq dataset describing the rod transcriptome of the zebrafish, which is now available as a resource for further studies of rod photoreceptor biology and comparative transcriptomics.
2018-02-08 | GSE100062 | GEO
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
Project description:Inherited retinal diseases and aged related macular degeneration are main causes of blindness that involves irreversible photoreceptor loss. Gene therapy approaches do not prevent photoreceptor degeneration during disease progression, and to date protocols for generating photoreceptors from pluripotent stem cells do not exist. Therefore, transplantation of photoreceptors containing retinal organoids is considered a potential option. However, in vitro formation of organoids requires animal-derived materials and they vary considerably in cell composition between batches, which strongly limits their applications in therapy. Here, we show that human recombinant retina-specific laminin isoform LN523, normally present in the extra cellular matrix ECM surrounding photoreceptors, supports differentiation of pluripotent embryonic stem cells to photoreceptor progenitors in vitro. Using a rabbit macular degeneration model, the transplanted and engrafted cells mature in vivo and form synaptic connectivity with the host retina. Furthermore, addition of a rod-derived cone viability factor increased the formation of cone photoreceptors. These results may pave the way for cell therapy treatment of macular degeneration.
2023-03-26 | GSE161414 | GEO