Dataset Information

The SNARE Regulator Complexin3 is a Target of the Cone Circadian Clock in the Mouse Retina

ABSTRACT: Purpose: The goals of this study are to evaluate the impact of the removal of the key circadian clock component BMAL1 on the transcriptome of cone photoreceptors Methods: Cone mRNA profiles of adult wild-type (WT, HRGPcre;Bmal1f/+) and cone-specific BMAL1 (HRGPcre;Bmal1f/f or cone-Bmal1−/−) mice were generated by deep sequencing, in triplicate, using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays Results: Comparison of the cone transcriptome between cone-Bmal1-/- and wild-type littermates at a single time point (middle of the light phase) revealed 88 genes differentially expressed (P < 0.05, fold change > 2). As expected, these 88 genes included known clock components but also genes known to be involved in a wide range of functions: gene regulation, neuron development and structure, protein binding, and transport. Conclusions: Our study represents the first detailed analysis of cone-BMAL1 transcriptomes, with biologic replicates, generated by RNA-seq technology. These data are consistent with the view that the cone clock controls many aspects of the development, maintenance, and function of the cones through its control of the transcriptome.

ORGANISM(S): Mus musculus

PROVIDER: GSE155550 | GEO | 2020/08/03

REPOSITORIES: GEO

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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.