Single-Cell RNA-Seq Reveals the Cellular Diversity and Developmental Characteristics of the Retinas of an Infant and a Young Child

Abstract

The human retina, located in the innermost layer of the eye, plays a decisive role in visual perception. Dissecting the heterogeneity of retinal cells is essential for understanding the mechanism of visual development. Here, we performed single-cell RNA-seq to analyze 194,967 cells from the donors of infants and young children, resulting in 17 distinct clusters representing major cell types in the retina: rod photoreceptors (PRs), cone PRs, bipolar cells (BCs), horizontal cells (HCs), amacrine cells (ACs), retinal ganglion cells (RGCs), Müller glial cells (MGs), microglia, and astrocytes (ASTs). Through reclustering, we identified known subtypes of cone PRs as well as additional unreported subpopulations and corresponding markers in BCs. Additionally, we linked inherited retinal diseases (IRDs) to certain cell subtypes or subpopulations through enrichment analysis. We next constructed extensive intercellular communication networks and identified ligand-receptor interactions that play crucial roles in regulating neural cell development and immune homeostasis in the retina. Intriguingly, we found that the status and functions of PRs changed drastically between the young children and adult retina. Overall, our study offers the first retinal cell atlas in infants and young children dissecting the heterogeneity of the retina and identifying the key molecules in the developmental process, which provides an important resource that will pave the way for research on retinal development mechanisms and advancements in regenerative medicine concerning retinal biology.

IL-4 induces reparative phenotype of RPE cells and protects against retinal neurodegeneration via Nrf2 activation

“…S 1 C, D). We further interrogated those immune cells into different types, including microglia/macrophage, NK/T cells, B cells, mast cells, and others with respective makers according to previous studies [ 25 , 27 , 28 ]. Interestingly, IL-4 was mainly expressed in microglia/macrophage (Fig.…”

“…It is noteworthy of the distribution pattern of IL-4 in normal retina indicating that IL-4 is likely derived from microglia based on the shape of IL-4-positive cells with filopodia-like protrusions, closely resembling those of branchy M2 phenotypes [ 27 , 28 ]. This is also consistent with the human scRNA-seq data (Fig.…”

A single-nucleus RNA sequencing atlas of the postnatal retina of the sharkScyliorhinus canicula

“…To assign a cell class identity to each cluster, we elaborated a list of marker genes reported in previous studies on other vertebrate species [11][12][13][14][15][18][19][20][21]23,[25][26][27][28][29][30][31]33,35,41 . Putative orthologues in the S. canicula genome were identified by comparing the sequence of the mouse gene (genome assembly GRCm39, GCF_000001635.27) 56 with the S. canicula genome assembly sScyCan1.1 (GCF_902713615.1) 51 using Blastn 57 .…”

Identification of biomarkers of bronchopulmonary dysplasia by single cell transcriptome sequencing technology and WGCNA：Data from bioinformatics analysis

“…Seurat is currently the dominant analysis tool for single-cell data [29]. Batch effects were processed using Seurat, enabling data from multiple samples to be combined.…”