Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

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

ABSTRACT: 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.

INSTRUMENT(S): BD FACSARIA III, Fluidigm C1, NextSeq 500

ORGANISM(S): Homo sapiens

SUBMITTER: Emily Welby

PROVIDER: E-MTAB-6058 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Isolation and Comparative Transcriptome Analysis of Human Fetal and iPSC-Derived Cone Photoreceptor Cells.

Welby Emily E Lakowski Jorn J Di Foggia Valentina V Budinger Dimitri D Gonzalez-Cordero Anai A Lun Aaron T L ATL Epstein Michael M Patel Aara A Cuevas Elisa E Kruczek Kamil K Naeem Arifa A Minneci Federico F Hubank Mike M Jones David T DT Marioni John C JC Ali Robin R RR Sowden Jane C JC

Stem cell reports 20171116 6

Loss of cone photoreceptors, crucial for daylight vision, has the greatest impact on sight in retinal degeneration. Transplantation of stem cell-derived L/M-opsin cones, which form 90% of the human cone population, could provide a feasible therapy to restore vision. However, transcriptomic similarities between fetal and stem cell-derived cones remain to be defined, in addition to development of cone cell purification strategies. Here, we report an analysis of the human L/M-opsin cone photorecept ...[more]

PMID: 29153988

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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.

Project description:Transcription factors have been implicated in the specification and differentiation of all cells in the mammalian retina with several transcription factors controlling the development of multiple neuronal subclasses. Horizontal cells and cone photoreceptors share a particularly intimate functional relationship but have been previously thought to develop through separate and distinct intrinsic molecular processes. We demonstrate that the zinc finger transcription factor Sall3 regulates development of both S-cone photoreceptors and horizontal cells. Our data shows that loss of function of Sall3 down-regulates the horizontal cell specific transcription factor Lhx1 and subsequently causes ectopic formation of horizontal-like wide-field amacrine cells partially phenocopying Lhx1-/- mice. Additionally, horizontal cells which laminate appropriately in Sall3 knockout mice show abnormal horizontal cell gene expression and failures in dendritic arborization. Over-expression of Sall3 also partially re-specifies cells to a horizontal-like wide-field amacrine fate. Intriguingly, Sall3 loss of function experiments also generated a massive reduction in the number of S-cone photoreceptors with remaining S-cones showing deficiencies in S-cone gene expression and morphology. Conversely, over-expression of Sall3 resulted in the ectopic expression of the S-cone specific genes S-opsin (Sop) and cone arrestin (Arr3) in electroporated cells. Our studies reveal that Sall3 regulates aspects of horizontal cell development in two ways: first, by maintaining Lhx1 expression, and second, by directly regulating expression of horizontal cell specific genes. We also show that Sall3 is an essential regulator of S-cone development in the mammalian retina and a potent activator of Sop and Arr3. Sall3 wild-type and knockout retinas used for explant cultures were extracted by microdissection at P0 in sterile PBS. Four cuts were made using micro-dissection scissors and the retinas were transferred to Nucleopore Track-Etch membrane filters (Whatman) and the tissue flattened out evenly. Filters were then floated on DMEM/F12, 10% FBS, 1X penicillin/streptomycin in 12 well plates and incubated at 37oC, 5% CO2 for 7 days. Three retinas (Sall3 knockout or wild-type) were pooled and RNA extracted using the Qiagen RNeasy kit. This was performed in triplicate for both wild-type and Sall3 knockouts retinas. A total of three replicates of Sall3 knockout and Sall3 wild-type RNA were analysed (six total samples).

Dataset Information

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

Publications

Isolation and Comparative Transcriptome Analysis of Human Fetal and iPSC-Derived Cone Photoreceptor Cells.

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