Comparative Transcriptome Analysis Of Cone Photoreceptors From Inherited Retinal Degeneration Mouse Models Using Single Cell Rna-Seq

Purpose : Cone photoreceptors (PR) play a critical role in vision as they are responsible for acuity and colour vision. Their dysfunction is behind vision loss in different types of inherited retinal degeneration (IRD). A complete understanding of the aberrant molecular and cellular processes that arise during these diseases is hampered by the relatively small proportion of cone cells the retina. In this study we have utilised advances in next generation sequencing to perform single cell RNA sequencing (scRNA-seq) on individual cone PR from three different mouse models of IRD to investigate transcriptional differences in cone cell survival and death.\r\n\r\nMethods : Retinas were collected at postnatal day 24 from two cone dystrophies (Pde6ccpfl1 and Gnat2cpfl5) and one rod-cone dystrophy (Pde6brd1) mouse models of IRD, in which cones were labelled with a green fluorescent reporter (GFP). FACS isolated GFP positive cones were collected in 96-well plates and processed for sequencing using 2×75 paired-end chemistry on an Illumina NextSeq, using a scRNA-seq process adapted from SMARTseq2 and MARS-seq approaches.\r\n\r\nResults : There were 118 differentially expressed (DE) genes common to all models and these were associated with gene ontology biological processes of histone modification and mitochondrial dysfunction. Interestingly, there were more similarities in expression profiles between the Gnat2cpfl5 and Pde6brd1 (139 DE genes, correlating with mitochondrial dysfunction) than compared to the two cone models (44 DE genes, associated with energy production and oxidation). Pathway analysis of exclusive DE profiles of each model (Gnat2cpfl= 290 genes; Pde6ccpfl1= 417 genes; Pde6brd1= 373 genes) revealed enrichment of pluripotency, mRNA processing and NF-κB signalling pathways within up-regulated genes, in contrast to down-regulated DE genes predominantly associated with the electron transport chain, oxidative phosphorylation and translation factors, respectively.\r\n\r\nConclusions : Cone-specific single cell RNA-seq of different IRD models revealed significant transcriptional differences both across different diseases and within each group, and highlighted the cell heterogeneity within cone-specific diseases.