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Single Cell Multiome Atlas of the Human Fetal Retina

ABSTRACT: As the light-sensing part of the visual system, the retina is comprised of five classes of neurons, including photoreceptors, horizontal, amacrine, bipolar, and retinal ganglion cells, along with several non-neuronal cell types such as Muller glia. These major cell classes can be further classified into hundreds of distinct cell subtypes. The development of the retina is under tight temporal control where multipotent progenitor cells differentiate into specific mature cell types in a sequential, but overlapping, order. Additionally, the developmental process is under tight spatial control, with cells at the central retina developing earlier than cells at the periphery. To provide a comprehensive view of the human fetal retina at the molecular level and investigate transcriptional regulatory mechanisms controlling the differentiation process, we profiled more than 300,000 single nuclei of the human fetal retina from 12 donors spanning post conception week 10 and 23 with Multiome RNA-seq and ATAC-seq.

ORGANISM(S): Homo sapiens

PROVIDER: GSE268630 | GEO | 2024/05/30

REPOSITORIES: GEO

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Project description:The vertebrate retina uses diverse neuronal cell types arrayed into complex neural circuits to extract, process and relay information from the visual scene to the higher order processing centers of the brain. Amacrine cells, a diverse class of inhibitory interneurons, are thought to mediate the majority of the processing of the visual signal that occurs within the retina. Despite morphological characterization, the number of known molecular markers of amacrine cell types is still much smaller than the 26 morphological types that have been identified. Furthermore, it is not known how this diversity arises during development. Here, we have combined in vivo genetic labeling and single cell genome-wide expression profiling to: 1) Identify specific molecular types of amacrine cells; 2) Demonstrate the molecular diversity of the amacrine cell class. It is difficult to identify new markers of amacrine cells, due to the fact that they only comprise a small percentage of the total cells in the retina. Additionally, given that there are at least 26 distinct types of amacrine cells, population based approaches fail to achieve the precision necessary to discover markers of each type. To facilitate the identification of new markers for different amacrine cell classes and to more fully characterize the molecular signatures of these classes, we isolated single amacrine cells. To accomplish this goal, we introduced genetic reporters (pNdrg4::GFP or pSynapsin::GFP) into the developing retina (P0) by either in vivo or ex vivo electroporation. These reporters were observed to label morphologically distinct sets of amacrine cells at the different timepoints harvested in this study. Electroporated retinas were then dissociated at different time points and single retinal amacrine cells were isolated by virtue of their GFP expression and placed in tubes containing lysis buffer. Then, their mRNAs were reverse transcribed, and the resulting cDNAs were PCR amplified for 35 cycles. Labeled cDNA samples were hybridized to Affymetrix 430 2.0 microarrays and the data was normalized using MAS5.0 software.

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Single Cell Multiome Atlas of the Human Fetal Retina

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