Transcriptional differential analysis of ocular surface ectoderm and surface ectoderm
10.3980/j.issn.1672-5123.2024.5.04
- VernacularTitle:眼表外胚层与表面外胚层转录组差异分析
- Author:
Lu SUN
1
,
2
;
Canwei ZHANG
1
,
2
;
Yuwen SONG
1
,
2
;
Jianxin LI
1
,
2
;
Lian DUAN
1
,
2
;
Yang GAO
1
,
2
;
Yuemei XIE
1
,
2
;
Luping WANG
1
,
2
;
Guangfu DANG
1
,
2
Author Information
1. Department of Ophthalmology, the First Affiliated Hospital of Shandong First Medical University, Jinan 250013, Shandong Province, China
2. Shandong First Medical University, Jinan 250117, Shandong Province, China
- Publication Type:Journal Article
- Keywords:
ocular surface ectoderm;
surface ectoderm;
transcriptome;
differential expressed genes;
signaling pathways
- From:
International Eye Science
2024;24(5):677-685
- CountryChina
- Language:Chinese
-
Abstract:
AIM:To identify transcriptional differences between the ocular surface ectoderm(OSE)and surface ectoderm(SE)using RNA-seq, and elucidate the OSE transcriptome landscape and the regulatory networks involved in its development.METHODS:OSE and SE cells were differentiated from human embryonic stem(hES)cells. Differentially expressed genes(DEGs)between OSE and SE were analyzed using RNA-seq. Based on the DEGs, we performed gene ontology(GO)analysis, Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway enrichment analysis, and protein-protein interaction(PPI)network analysis. Transcription factors(TFs)and hub genes were screened. Subsequently, TF-gene and TF-miRNA regulatory networks were constructed using the NetworkAnalyst platform.RESULTS:A total of 4 182 DEGs were detected between OSE and SE cells, with 2 771 up-regulated and 1 411 down-regulated genes in OSE cells. GO-BP analysis revealed that up-regulated genes in OSE were enriched in the regulation of ion transmembrane transport, axon development, and modulation of chemical synaptic transmission. Down-regulated genes were primarily involved in nuclear division, chromosome segregation, and regulation of cell cycle phase transition. KEGG analysis indicated that up-regulated genes in OSE cells were enriched in signaling pathways such as cocaine addiction, axon guidance, and amphetamine addiction, while down-regulated genes were enriched in proteoglycans in cancer, ECM-receptor interaction, protein digestion and absorption, and cytokine-cytokine receptor interaction. Additionally, compared with SE, 204 TFs(including FOS, EGR1, POU5F1, SOX2, and PAX6)were up-regulated, and 80 TFs(including HAND2, HOXB6, HOXB5, HOXA5, and HOXB8)were down-regulated in OSE cells. Furthermore, we identified 6 up-regulated and 9 down-regulated hub genes in OSE cells, and constructed TF-gene and TF-miRNA regulatory networks based on these hub genes.CONCLUSIONS:The transcriptome characteristics of OSE and SE cells were elucidated through RNA-seq analysis. These findings may provide a novel insight for studies on the development and in vitro directed induction of OSE and corneal epithelial cells.
