Single-cell RNASeq analysis of human retinal organoids generated from hiPSC derived of a healthy donor patient
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ABSTRACT:
PROVIDER: PRJNA728798 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR14493244.fastq.gz | Fastqsanger.gz |
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Project description:Results: Our histologic studies indicated that human retinal organoids (HROs) at day 200 of differentiation in this system are postmitotic and thus completed retinogenesis. Further, HRO contain all major retinal cell types in a laminated structure. Notably, HROs are cone photoreceptor-rich, show a 1:1:1 ratio of Müller glia, rod and cone photoreceptor. Immunostaining and ultrastructural studies showed that photoreceptors neurons mature, including photoreceptor inner and nascent outer segment formation. Our transcriptome analysis at the single cell level supports these findings. Further, comparison with published datasets (Voigt et al. 2019 [PMID: 31075224]) indicate that the genotype of cone photoreceptors in this HRO system correlates more strongly with the foveal cones of the human primary retina than peripheral cones. Müller glia show a trend towards human fovea whereas rod photoreceptors were found to be nearly similar. Conclusions: Single cell transcriptome analysis of HROs support and extend our findings at the histological level, indicating that HROs are cone photoreceptor-rich, and provide some characteristics of the human macula.
2022-09-01 | GSE174215 | GEO
Project description:We generated hiPSCs from patients fibloblast with retinitis pigmentosa (RP) using retrovirus and Sendai virus vectors, which we differentiated into hiPSC derived retinal pigment epithelium using two different methods (SDIA and SFEB methods). We investigated whether these hiPSC-RPE colonies, which were differentiated from various cell lines and methods, showed similar gene expression patterns to those of native RPE. We classified hiPSC-RPE, hiPSCs, and fibroblasts from RP patients, hRPE (commercially available human fetal RPE, Lonza) , ARPE19 (a human RPE cell line), and other human tissues from 54,675 probe sets using microarray data.
2014-11-03 | E-GEOD-50738 | biostudies-arrayexpress
Project description:Proteogenomic analysis of three stem cell samples from a healthy donor. The cell lines used here are commercially available as induced pluripotent stem cells (iPSC) via retroviral reprogramming of skin fibroblasts isolated from the PGP1 donor from the Personal Genome Project (PGP) (Coriell, GM23338). hiPSC cultures were maintained as previously described [doi.org/10.1387/ijdb.230220lg]. Cell lysis, protein extraction, trypsin digestion, and peptide desalting were performed using the AccelerOme automated system from Thermo Fisher Scientific according to the manufacturer's instructions.
Peptides were separated on a 110 cm micro-PAC HPLC column (Thermo Fisher Scientific) with a Vanquish Neo HPLC system (Thermo Fisher Scientific) coupled through a nano-electrospray source to a Tribrid Ascend mass spectrometer (Thermo Fisher Scientific) with a non-linear gradient of 1 - 50 % buffer B (0.1 % formic acid, 80 % acetonitrile) at a flow rate of 300 nL/min over 160min. The column temperature was kept at 50 C. Samples were acquired using a DDA MS2 data acquisition, where the Tribrid mass spectrometer was switching between a full scan (120 K resolution, Auto max. injection time, AGC target 100%), to a data-dependent (Top-20) MS/MS scans in the Orbitrap analyzer (15K resolution, 27 ms max. injection time, AGC target 400%). Isolation window was set to 1.4 (m/z), and normalized collision energy to 25. Precursors were filtered by charge state of 2-6 and multiple sequencing of peptides was minimized by excluding the selected peptide candidates for 60 s.
Protein sequence database was generated by ProHap [doi.org/10.1101/2023.12.24.572591] using the phased genotype of the healthy donor, available from [https://my.pgp-hms.org/profile_public?hex=hu43860C].
2024-07-03 | MSV000095226 | MassIVE
Project description:We generated hiPSCs from patients fibloblast with retinitis pigmentosa (RP) using retrovirus and Sendai virus vectors, which we differentiated into hiPSC derived retinal pigment epithelium using two different methods (SDIA and SFEB methods). We investigated whether these hiPSC-RPE colonies, which were differentiated from various cell lines and methods, showed similar gene expression patterns to those of native RPE.
2014-11-03 | GSE50738 | GEO
Project description:The application potential of human induced pluripotent stem cells (hiPSC) derived human retinal organoids (HRO) relies on the robustness and transferability of the methodology for their generation. Standardized strategies and parameters to effectively assess, compare and optimize organoid protocols have been started to be established, but are not completed yet. To advance this, we explored the efficiency and reliability of a differentiation protocol that facilitates retina generation by formation of neuroepithelial cysts from hiPSC clusters. Here, we tested seven different hiPSC lines, which reproducibly generated HROs. Histologic and ultrastructural analyses support regulated HRO differentiation and maturation. The different hiPSC lines appeared to be a larger source of variance than experimental rounds. Whereas previous reports showed that HRO in several other protocols contain a rather low numbers of cones compared to rods, HROs derived by the cyst protocol consistently are cone-richer and with an comparable ratio of cones, rods, and Müller glia. Additionally, we devised a potential strategy to systematically evaluate different protocols side-by-side through parallel differentiation from the same hiPSC batches: The cyst-protocol was compared to a conceptually different protocol based on cell aggregate formation from single hiPSCs. Comparison of four hIPSC lines showed that both protocols reproduced key characteristics of retinal epithelial structure and cell composition, but the cyst-protocol provided a higher HRO yield. Further, while cyst-derived HROs maintained stable at least up to date 250, whereas single hiPSC-derived HROs showed spontaneous pathologic changes already by day 200. Overall, our data provide insight into the efficiency, reproducibility, and stability of the cyst-protocol for HRO generation, which will be useful for further organoid system optimization, as well as basic and translational research applications.
2023-09-26 | GSE237007 | GEO
Project description:Purpose: To identify transcriptomic features of hiPSC-derived cells with a good capability to generate retinal organoids Methods: Human induced pluripotent stem cell (hiPSC) samples were collected at two time points for RNA sequencing (day zero and seven, each time point in triplicate). Cell pellets were collected and flash frozen. Total RNA was extracted by a phenol/chloroform method using TRIzol LS reagent (ThermoFisher Scientific, MA) according to the manufacturer's guidelines. tRNA was treated with DNAse I prior to library preparations being performed for RNAsequencing. Results: Human iPSC lines show variation in their ability to differentiate into a neuroectodermal/early eye field phenotype. This study identified a panel of signature transcripts that were differentially expressed at seven days of differentiation, between lines of low- and high-retinal propensity. Conclusions: This study provides a gene profile that identifies which hiPSC-derived cells have a good capability to generate retinal organoids. This allows for the analysis of retinal propensity by quantitative PCR within the first seven days of differentiation.
2023-06-21 | GSE192665 | GEO
Project description:Consistent with clinical observations that posterior uveitis frequently involves the retinal vasculature and recent recognition of vascular heterogeneity, we hypothesized that retinal vascular endothelium was a cell population of unique molecular phenotype. Donor-matched cultures of primary retinal and choroidal endothelial cells from 6 human cadavers were incubated with either Toxoplasma gondii tachyzoites (10:1, parasite:cell) or Escherichia coli lipopolysaccharide (100 ng/mL); control cultures were simultaneously incubated with medium. Gene expression profiling of endothelial cells was performed using oligonucleotide arrays containing probes designed to detect 8747 human transcripts. After normalization, differential gene expression was assessed by the significance analysis of microarrays, with the false discovery rate set at 5 %. For selected genes, differences in level of expression between retinal and choroidal cells were evaluated by real-time RT-PCR. Graphical descriptive analysis demonstrated strong correlation between gene expression of unstimulated retinal and choroidal endothelial cells, but also highlighted distinctly different patterns of expression that were greater than differences noted between donors or between unstimulated and stimulated cells. Overall, 779 of 8,747 transcripts (8.9 %) were differentially represented. Notably, the 330 transcripts that were present at higher levels in retinal cells included a larger percentage of transcripts encoding molecules involved in the immune response. Differential gene expression was confirmed for 12 transcripts by RT-PCR. Retinal and choroidal vascular endothelial cells display distinctive gene expression profiles. Our findings suggest the possibility of treating posterior uveitis by targeting specific interactions between the retinal endothelial cell and an infiltrating leukocyte. Experiment Overall Design: Retinal and choroidal vascular endothelial cells were isolated from both eyes of 6 human cadaver donors. Endothelial cells of each subtype from each donor were separately pooled and cultured. In a first series of experiments (Experiment 1), donor-matched cultures of retinal and choroidal endothelial cells derived from 3 donors were incubated with either T. gondii tachyzoites or medium alone. In a second set of experiments (Experiment 2), cultured retinal and choroidal endothelial cells derived from the other 3 donors were stimulated with LPS or medium alone. Whenever possible, 2 replicate dishes of endothelial cells were subjected to each set of conditions. Subsequent to incubations, mRNA was extracted from a cell lysate prepared from each dish of cells, and cRNA derived from each mRNA preparation was separately hybridized to one oligonucleotide expression array.
2008-06-15 | E-GEOD-7850 | biostudies-arrayexpress
Project description:The loss of cone photoreceptor cells, which are critical for optimal daylight vision, have the great impact on vision during retinal degenerations. Retinal differentiation of human induced pluripotent stem cell (hiPSC) sources could provide a renewable source of cone photoreceptors towards developing a cone cell replacement therapy to treat blindness. Demonstration of comparable gene expression profiles between human foetal and stem cell-derived cones at equivalent stages is required to progress the cell transplantation approach into the patient, as it is hypothesised stem cell-derived cones are required to show high levels of developmental recapitulation of the in vivo generated cones. In this study, the AAV2/9.pR2.1.GFP reporter was used to specifically label L/M-opsin cone photoreceptors in human foetal retinal samples, obtained from the MRC-Wellcome Trust Human Developmental Biology Resource, at a range of developmental stages. The L/M-opsin cone population represent the majority cone cell types in the adult human retina and are the only photoreceptors present within the fovea. Using fluorescence activated cell sorting, L/M-opsin GFP+ cones and GFP- retinal populations, alongside total foetal retinal samples containing all retinal cell tytpes, were isolated and processed for bulk RNA sequencing and downstream comparative analysis. Using DESeq2 differential gene expression analyses, statistically significant genes enriched within the GFP+ human foetal LM-opsin cone populations were determined which led to the identification of a cone enriched gene signature of human L/M-opsin cone photoreceptors. The AAV2/9.pR2.1.GFP reporter was applied to hiPSC-derived retinal cultures to isolate and process cone-like cell populations for RNA sequencing using the same strategy developed within the human foetal retina. Applying the cone enriched gene signature to the transcriptome of hiPSC-derived GFP+ samples at equivalent developmental stages revealed some expression similarities in genes found to be enriched within the late foetal L/M-opsin cone photoreceptors. This analysis overall revealed an intermediate stage of cone differentiation was achieved within the hiPSC-derived samples and the comparison to human foetal L/M-opsin gene express profiles suggesting further differentiation of hiPSC-derived sample is required.
2018-04-20 | E-MTAB-6057 | biostudies-arrayexpress
Project description:For in vitro disease modeling of LDS, we used healthy donor cells (TGFBR1+/+), and generated heterozygote (TGFBR1A230T/+), and homozygote (TGFBR1A230T/A230T) knock-in clones using CRISPR-Cas9 gene editing. We also generated hiPSC from peripheral blood mononuclear cells harvested from an LDS patient, and corrected the mutation in the patient-derived hiPSC. To address the lineage-specific effects of TGFBR1A230T, and SMAD3c.652delA/+, hiPSC were differentiated into cardiovascular progenitor cell-derived smooth muscle cells (CPC-SMC), and neural crest stem cell-derived smooth muscle cells (NCSC-SMC) using in vitro differentiation protocols. We performed large-scale single cell profiling of the resulting CPC-SMC and NCSC-SMC.
2021-08-04 | GSE175647 | GEO
Project description:Reliability of human retinal organoid generation from hiPSC-derived neuroepithelial cysts
| PRJNA993408 | ENA