Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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RNA-seq of isolated human foetal and hiPSC L/M-opsin cone photoreceptor populations labelled using the AAV2/9.pR2.1.GFP reporter

ABSTRACT: 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.

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Homo sapiens

SUBMITTER: Jane Sowden

PROVIDER: E-MTAB-6057 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Human cone photoreceptors represent a rare cell population of the human retina and are largely outnumbered by other retinal cell types. Despite their rarity, cone photoreceptors are critical for optimal daylight vision and their loss has the greatest impact on sight during the progression of retinal dystrophies. This is most applicable to the L/M-opsin cone populations which form the largest proportion of cones in the human retina and are the only cone types present within the fovea, which is responsible for fine detailed vision. Better understanding of the early genesis of these cells within the human developing retina, particularly in relation to the expression of genes that could be involved in regulating early events such as cell fate decision, is required. These molecular determinants could be exploited in vitro to generate more cone photoreceptors within human stem cell-derived retinal differentiation culture systems, suitable for use in cell transpantation therapies or disease modelling purposes. Additionally, the nature of this cell population in terms of their gene expression heterogeneity remains to be defined. State of the art technology has now advanced so that mRNA sequencing can be performed on individual cells, which means the transcriptome of rare cell populations such as cone photoreceptor cells can be interrogated without the need for ample material. Using the AAV2/9 pR2.1:GFP reporter, containing a synthetic promoter region previously characterised to drive expression in cone photoreceptors, we label and isolate human foetal L/M-opsin cone photoreceptors within the 15pcw human retinal retina. Isolated GFP+ cells were separated into individual cells using the Fluidigm C1 microfludics system, before RNA extraction and cDNA library preparation was performed. In total, 74 single cells were captured and processed for RNA sequencing; quality control of the data led to the inclusion of 65 individual cells for the downstream analysis. Principal component analysis revealed a very subtle heterogeneity across the cells, with the highest variability observed according to the first principal component (PC1). Differential gene expression analysis correlated to PC1 led to the identification of 503 significantly differentially expressed genes. Notably, some genes increase in expression across the cells when ordered according to PC1 which have previous associations with photoreceptor maturation, whereas other genes associated with developmental processes became downregulated across the cells. This led to the hypothesis that at this single timepoint in the human foetal retina, developing L/M-opsin cone photoreceptors exist at different stages of maturation. Overlapping genes were identified from comparing RNA seq data from 15pcw single cells and population samples at early and late timepoints of pR2.1:GFP+ cells, which showed the same gene expression trend between experiments. This suggests differences in cell maturation at a single timepoint of development could be representative of their true developmental trajectory. This overlapping gene dataset is also highly useful to define new gene that could be involved in cone photoreceptor development.

Dataset Information

RNA-seq of isolated human foetal and hiPSC L/M-opsin cone photoreceptor populations labelled using the AAV2/9.pR2.1.GFP reporter

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