The Advance of Single-Cell RNA Sequencing Applications in Ocular Physiology and Disease Research

Abstract

The eye, a complex organ essential for visual perception, is composed of diverse cell populations with specialized functions; however, the complex interplay between these cellular components and their underlying molecular mechanisms remains largely elusive. Traditional biotechnologies, such as bulk RNA sequencing and in vitro models, are limited in capturing cellular heterogeneity or accurately mimicking the complexity of human ophthalmic diseases. The advent of single-cell RNA sequencing (scRNA-seq) has revolutionized ocular research by enabling high-resolution analysis at the single-cell level, uncovering cellular heterogeneity, and identifying disease-specific gene profiles. In this review, we provide a review of scRNA-seq application advancement in ocular physiology and pathology, highlighting its role in elucidating the molecular mechanisms of various ocular diseases, including myopia, ocular surface and corneal diseases, glaucoma, uveitis, retinal diseases, and ocular tumors. By providing novel insights into cellular diversity, gene expression dynamics, and cell-cell interactions, scRNA-seq has facilitated the identification of novel biomarkers and therapeutic targets, and the further integration of scRNA-seq with other omics technologies holds promise for deepening our understanding of ocular health and diseases.

Keywords: biomarker; cellular heterogeneity; ocular disease; ocular physiology; single-cell RNA sequencing.

Figure 1

Schematic diagram of the scRNA-seq workflow. ① The specific eye tissue is collected and undergoes digestion to make the cell suspension. Each cell is labeled with a unique barcode during cDNA synthesis, and the cDNA library is constructed. Amplified libraries are submitted for scRNA-seq and the reads are aligned to a reference genome; the sequencing data are visualized and analyzed. ② Cell analysis is the main part of scRNA-seq study, commonly including cell subtype proportion, cell subtype difference, cell interaction, cell communication, pseudotime analysis, etc. ③ Gene analysis is a common and important part of scRNA-seq research, mainly including differentially expressed genes, functional enrichment analysis, protein–protein interactions, etc. Created in BioRender. Cheng, Y. (2025) https://BioRender.com/g23y304.

Figure 2

The main application of scRNA-seq in ocular research includes ocular tissue development, physiology, and ocular diseases. By Figdraw (https://www.figdraw.com/#/).

Figure 3

Important prospects of scRNA-seq application in ocular research include ocular development, ocular diseases, multi-omics integration, and therapeutic target exploration. Created in BioRender. Cheng, Y. (2025) https://BioRender.com/m79w206.