Single-Cell RNA Sequencing: Opportunities and Challenges for Studies on Corneal Biology in Health and Disease

Abstract

The structure and major cell types of the multi-layer human cornea have been extensively studied. However, various cell states in specific cell types and key genes that define the cell states are not fully understood, hindering our comprehension of corneal homeostasis, related diseases, and therapeutic discovery. Single-cell RNA sequencing is a revolutionary and powerful tool for identifying cell states within tissues such as the cornea. This review provides an overview of current single-cell RNA sequencing studies on the human cornea, highlighting similarities and differences between them, and summarizing the key genes that define corneal cell states reported in these studies. In addition, this review discusses the opportunities and challenges of using single-cell RNA sequencing to study corneal biology in health and disease.

Deciphering the heterogeneity of differentiating hPSC-derived corneal limbal stem cells through single-cell RNA sequencing

“…Single-cell RNA sequencing (scRNA-seq) allows deciphering the heterogeneity of complex cellular systems and can serve as a powerful tool for assessing the efficiency of hPSC differentiation protocols ( Cuomo et al., 2020 ). In recent years, the use of scRNA-seq has significantly expanded our knowledge about cell types in the cornea in vivo ( Arts et al., 2023 ), but it is not yet widely applied for hPSC differentiation to LSCs. Through years of dedicated work on hPSC-LSC differentiation in our laboratory, we have obtained promising results using traditional characterization methods such as immunofluorescence (IF) staining ( Hongisto et al., 2017 ; Vattulainen et al., 2019 ; 2021 ).…”

Deciphering the heterogeneity of differentiating hPSC-derived corneal limbal stem cells through single-cell RNA-sequencing

“…In recent years, the use of scRNA-seq techniques has significantly expanded our knowledge about the LSC identity and limbal progenitor distribution on the multistage corneal differentiation trajectory in vivo (e.g., Collin et al, 2021; Dou et al, 2021; Li et al, 2021; Ligocki et al, 2021). The corneal atlas generated from these works also forms a valuable up-to-date reference for the hPSC-derived LSCs (for a comprehensive recent review, see Arts et al, 2023).…”

An atlas of immune cell transcriptomes in human immunodeficiency virus-infected immunological non-responders identified marker genes that control viral replication

“…High-throughput, single-cell RNA sequencing (scRNAseq) has emerged as a prominent tool in transcriptomicbased investigations of human diseases. [16][17][18][19] This procedure enables the determination of transcriptional disparities in cell subpopulations and even the identification of novel cell subtypes at single-cell resolution. The utilization of scRNA-seq has been employed in transcriptomic studies related to HIV-1 replication and infection, latent HIV-1 reservoirs, and lymphoid tissues in HIV-infected individuals.…”