Molecular characteristics and spatial distribution of adult human corneal cell subtypes

Abstract

Bulk RNA sequencing of a tissue captures the gene expression profile from all cell types combined. Single-cell RNA sequencing identifies discrete cell-signatures based on transcriptomic identities. Six adult human corneas were processed for single-cell RNAseq and 16 cell clusters were bioinformatically identified. Based on their transcriptomic signatures and RNAscope results using representative cluster marker genes on human cornea cross-sections, these clusters were confirmed to be stromal keratocytes, endothelium, several subtypes of corneal epithelium, conjunctival epithelium, and supportive cells in the limbal stem cell niche. The complexity of the epithelial cell layer was captured by eight distinct corneal clusters and three conjunctival clusters. These were further characterized by enriched biological pathways and molecular characteristics which revealed novel groupings related to development, function, and location within the epithelial layer. Moreover, epithelial subtypes were found to reflect their initial generation in the limbal region, differentiation, and migration through to mature epithelial cells. The single-cell map of the human cornea deepens the knowledge of the cellular subsets of the cornea on a whole genome transcriptional level. This information can be applied to better understand normal corneal biology, serve as a reference to understand corneal disease pathology, and provide potential insights into therapeutic approaches.

Single cell RNA-seq of human cornea organoids identifies cell fates of a developing immature cornea

“…In this study, we performed concurrent scRNA-seq analyses of three human iPSC-derived cornea organoids and full-thickness central corneas from three different adult human donors. Our human corneal dataset corroborated recent transcriptomic studies of the full thickness human cornea ( 10 , 44 ). Human cornea organoids have not been analyzed at the single cell transcriptomic level.…”

Differentiation Trajectory of Limbal Stem and Progenitor Cells under Normal Homeostasis and upon Corneal Wounding

“…Recently, due to the development of the technology of single-cell RNA sequencing and single-cell quantitative real-time PCR, researchers were able to analyze limbal epithelial cells at the single-cell level. Many studies were performed on human corneas from healthy and keratoconus samples and suggested more than one clusters (heterogeneity) as putative limbal stem/progenitor cells with characteristic markers [16][17][18][19]. The studies using human samples provided more human/clinical related data but have the disadvantages of significant sample variation due to the non-uniform genetic background of different donors, which makes it difficult to compare the data from different donors (e.g., among healthy corneas, between healthy corneas and pathological corneas).…”

Molecular Characteristics and Distribution of Adult Human Corneal Immune Cell Types

“…On the ocular surface, the cornea is a unique and highly specialized tissue that is avascular and transparent in order to allow light to be transmitted for vision. Recent studies have identified cell types in the cornea using scRNA-seq; however, they primarily paid attention to epithelial and stromal cells, the major cell types in the cornea ( 19 , 25 , 26 ). In this study, we concentrated on the immune cell types and observed seven distinct immune cell clusters that differed in function.…”