Sequencing of Induced pluripotent stem cell derived retinal progenitor cells
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ABSTRACT:
PROVIDER: PRJNA590151 | ENA |
REPOSITORIES: ENA
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Project description:Age-related macular degeneration (AMD) is a result of degeneration/damage of the retinal pigment epithelium (RPE) while retinitis pigmentosa (RP), an inherited early-onset disease, results from premature loss of photoreceptors. A promising therapeutic approach for both is the replacement of lost/damaged cells with human induced pluripotent stem cell (hiPSC)-derived retinal cells. We studied the chemistry of retinal progenitor cells derived from iPSC through our patented unified differentiation protocol with the aim to take the cells for clincal benefits to needly patients. RPE expressed tight junction proteins, showed pigmentation and ciliation, and secreted polarization-related factors vascular endothelial growth factor (VEGF) and pigment epithelium-derived factor (PEDF). PRP expressed neural retina proteins and cone and rod markers, and responded to KCl-induced polarization. Transcriptomic analysis demonstrated an increase in the expression of mature retinal tissue-specific genes coupled with concomitant downregulation of genes from undesired lineages. RPE transplantation rescued visual function in RCS rats shown via optokinetic tracking and photoreceptor rescue. PRP transplantation improved light perception in NOD.SCID-rd1 mice, and positive electroretinography signals indicated functional photoreceptor activity in the host's outer nuclear layer. Graft survival and integration were confirmed using immunohistochemistry, and no animals showed teratoma formation or any kind of ectopic growth in the eye.
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Project description:Genomic characterization of sub-populations in human pluripotent stem cell-derived retinal progenitor cells that drive retinal layer structure
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Project description:Embryonic stem cells are pluripotent and possess the ability to differentiate into numerous lineages during the developmental process. In similarity to embryonic stem cells, human induced pluripotent stem cells (iPSCs) possess the potential to differentiate into multiple lineages making them an excellent research tool. We generated iPSCs from multiple donors and also differentiated iPSCs from these donors into human neural progenitor cells (NPCs). We used human transcriptome arrays to detail the programme of gene expression underlying NPC induction and identified distinct classes of up-regulated genes during this process. Total RNAs were extracted from human induced pluripotent stem cells and induced pluripotent stem cell-derived neural progenitor cells. Their gene expression profiles were investigated using the Affymetrix GeneChip Human Transcriptome Array 2.0 platform.
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Project description:Extracellular vesicles are bubbles used by cells for intercellular and intertissue interactions. Their cargo includes various proteins, nucleic acids, peptides, which, interacting with cells, trigger intracellular cascades. Proteomic analysis of extracellular vesicles from different cell types has already been performed. Here, we present the first proteomic analysis of extracellular vesicles proteins obtained from three lines of glial progenitor cells differentiated from human induced pluripotent stem cells.
2025-12-15 | PXD067360 | Pride
Project description:Microarray anlaysis was performed to investigate gene expression patterns of other transcription factors involved in early retinal and/or forebrain development using human embryonic stem cell-derived retinal and forebrain progenitor cells. After 20 days of differentiation, vesicular neurospheres selectively expressed multiple retinal transcription factor genes appropriate for the OV stage of retinogenesis, whereas nonvesicular neurospheres expressed transcription factors indicative of the embryonic forebrain. Many transcription factor genes associated with retinal development were present at higher levels in vesicular vs. nonvesicular neurospheres. Nonvesicular neurospheres, on the other hand, expressed higher levels of transcription factors implicated in early forebrain development. Taken together, results indicated that the vesicular and nonvesicular neurospheres harbored retinal progenitor cells and early forebrain populations, respectively. Compare the global gene expression of retinal progenitor cells and forebrain progenitor cells derived from human embryonic stem cells
2011-12-01 | E-GEOD-29237 | biostudies-arrayexpress
Project description:This study examines and compares the protein content in conditioned media collected from neural cell types generated from human pluripotent stem cells. Conditioned media was prepared for 48 hours at a final endpoint of differentiation day 12. Both groups are from parental line WTC11 and cultured as a monolayer on matrigel. Both groups contain a transgene cassette for doxycycline-inducible expression of sox9 and nfia. Doxycycline was only included in the iAstro groups, whereas it was omitted in the neural progenitor cell groups.
2022-01-19 | PXD030821 | Pride
Project description:The mechanisms of layer formation of retinal spheroids were investigated using Rax::GFP-positive retinal progenitor cells (RPCs) obtained from human embryonic stem cell-derived retinal organoids. Single-cell RNA sequencing revealed that well-layered spheroids exhibited a transient activation of canonical WNT2B–FZD7 signaling followed by a temporary expression of non-canonical WNT5A, processes associated with the formation of organized retinal layers. Despite structural differences in vitro, both non-layered and well-layered retinal spheroids of differentiation day 60 successfully developed into each cone and rod subtypes of photoreceptors and established synaptic connections with host bipolar cells after transplantation in retinal degeneration model rats, resulting in light-evoked functional recovery. Additionally, part of the presumable RPCs differentiated into non-retinal lineages, including ciliary marginal zone-like, retinal pigment epithelium-, and spinal cord-like tissues in vitro, reflecting the developmental plasticity of RAX-positive cells. These findings suggest that canonical and non-canonical WNT signaling pathways sequentially orchestrate early retinal morphogenesis, while environmental factors within the host retina strongly drive the alignment and functional integration of graft photoreceptors.
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Project description:Human induced pluripotent stem cells (hIPSCs) represent a unique opportunity for regenerative medicine since they offer the prospect of generating unlimited quantities of cells for autologous transplantation as a novel treatment for a broad range of disorders. It is now known that primary iPS cells often carry genomic aberrations and these abnormality may compromise their possibility of clinical application. We analysed primary hIPSC lines derived from monoclonal human endothelial progenitor cell lines by array-based comparative genomic hybridisation.
2014-04-04 | E-MTAB-1319 | biostudies-arrayexpress
Project description:This study investigates the differentiation of retinal ganglion cells (RGCs) from human pluripotent stem cells (hPSCs) to optimise and characterise in-vitro RGC generation. Retinal organoids were derived from a human embryonic stem cell line (H9) and a laboratory-established human induced pluripotent stem cell (hiPSC) line. For each stem cell line, two independent passages of cells were generated as biological replicates (n = 2 per line). To assess transcriptional diversity and differentiation efficiency, organoids were harvested at day 40 of differentiation, dissociated into single cells, and cultured for an additional 14 days to enrich for RGCs. Following enrichment, single-cell suspensions were processed using the 10x Genomics Chromium platform and sequenced on an Illumina NovaSeq X Plus. The resulting single-cell transcriptomes provide a molecular snapshot of RGC differentiation from hPSCs and enable comparison between hESC- and hiPSC-derived retinal lineages. The data contribute to refining differentiation protocols and improving reproducibility of stem-cell-derived retinal models. Raw BCL files were processed at the Australian Genome Research Facility (AGRF) using Illumina’s standard pipeline to generate FASTQ files. FASTQs were additionally processed with Cell Ranger v7.1.0 (10x Genomics) using the GRCh38/Ensembl v109 reference to produce unfiltered gene-by-cell UMI count matrices in standard 10x sparse format (barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz), which are provided as processed data in this submission. Raw FASTQ files are also archived in this ArrayExpress submission.
2026-05-30 | E-MTAB-16297 | biostudies-arrayexpress
Project description:Embryonic stem cells are pluripotent and possess the ability to differentiate into numerous lineages during the developmental process. In similarity to embryonic stem cells, human induced pluripotent stem cells (iPSCs) possess the potential to differentiate into multiple lineages making them an excellent research tool. We generated iPSCs from multiple donors and also differentiated iPSCs from these donors into human neural stem/progenitor cells (NSCs). We used human transcriptome arrays to detail the programme of gene expression underlying NPC induction and identified distinct classes of up-regulated genes during this process. Human induced pluripotent stem cells (iPSCs) can be used to create neurons in vitro. This microarray allows researchers to check the expression of their gene of interest in iPSC-derived neurons and compare the gene expression profile of iPSC-derived neurons to other cell types or primary human tissue.
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