Identification of Human Retinal Organoid Cell Differentiation-Related Genes via Single-Cell Sequencing Data Analysis

Comput Math Methods Med. 2022 Aug 8;2022:9717599. doi: 10.1155/2022/9717599. eCollection 2022.

Abstract

Objective: To study the development process of the human retina, we analyzed the development track of main cell types and transitional cell populations, identifying the retinal organoid cell differentiation-related genes (RDRGs).

Methods: Single-cell RNA sequencing data (scRNA-Seq) of human retinal organoids were downloaded from Gene Expression Omnibus (GEO) database in this study. Data were processed with quality analysis and analysis of variance. Principal component analysis and t-distributed stochastic neighbor embedding were used to conduct dimension reduction analysis and type annotation for the screened data. Marker genes and RDRGs were identified by differential analysis. Cell differentiation characteristics were determined by trajectory analysis. Enrichment pathways were analyzed by Gene Ontology(GO) and Kyoto Encyclopedia of Genes and Genomes(KEGG), and functional modules were obtained by protein-protein interaction (PPI) network analysis.

Results: iPSCs were mainly located at the root of differentiation trajectory, while neurons and astrocytes were distributed in different branches, respectively. Meanwhile, 220 RDRGs were obtained. They were involved in the biological functions related to vision and visual development, as well as significantly enriched in signaling pathways associated with retinal vascular development and retinal neuroregulation. Protein-protein interaction network construction and functional subnetwork analysis were conducted on RDRGs, and two functional submodules were obtained. The enrichment analysis presented that the two submodules played a vital role in retinal development, visual perception, and cell respiration.

Conclusions: This study identified RDRGs and revealed the biological functions involved in these genes, which are expected to provide evidence for researching retinal development and diseases.

MeSH terms

  • Cell Differentiation / genetics
  • Computational Biology / methods
  • Data Analysis
  • Gene Expression Profiling / methods
  • Gene Regulatory Networks
  • Humans
  • Neurons
  • Organoids*
  • Retina
  • Single-Cell Analysis*