Department of Ophthalmology, Dalian No. 3 People's Hospital, Dalian 116033, China.
Department of Blood Purification, Affiliated Zhongshan Hospital of Dalian University, Dalian 116001, China.
Comput Math Methods Med. 2022 Aug 8;2022:9717599. doi: 10.1155/2022/9717599. eCollection 2022.
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).
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 -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.
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.
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.
为了研究人类视网膜的发育过程，我们分析了主要细胞类型和过渡细胞群体的发育轨迹，鉴定了视网膜类器官细胞分化相关基因（RDRGs）。
本研究从基因表达综合数据库（GEO）下载了人类视网膜类器官的单细胞 RNA 测序数据（scRNA-Seq）。对数据进行质量分析和方差分析处理。采用主成分分析和 t-分布随机邻域嵌入进行筛选数据的降维和类型注释。通过差异分析鉴定标记基因和 RDRGs。通过轨迹分析确定细胞分化特征。通过基因本体论（GO）和京都基因与基因组百科全书（KEGG）分析富集途径，并通过蛋白质-蛋白质相互作用（PPI）网络分析获得功能模块。
iPSC 主要位于分化轨迹的根部，而神经元和星形胶质细胞分别分布在不同的分支上。同时，获得了 220 个 RDRGs。它们参与了与视觉和视觉发育相关的生物学功能，并且在与视网膜血管发育和视网膜神经调节相关的信号通路中显著富集。对 RDRGs 进行蛋白质-蛋白质相互作用网络构建和功能子网络分析，得到了两个功能子模块。富集分析表明，这两个子模块在视网膜发育、视觉感知和细胞呼吸中起着重要作用。
本研究鉴定了 RDRGs，并揭示了这些基因所涉及的生物学功能，有望为研究视网膜发育和疾病提供依据。
