Transcriptome analysis identifies the differentially expressed genes related to the stemness of limbal stem cells in mice

Zhi Hou Guo; Yang Yan Sheng Jia; Yi Ming Zeng; Zhao Fa Li; Jun Sheng Lin

doi:10.1016/j.gene.2021.145447

Transcriptome analysis identifies the differentially expressed genes related to the stemness of limbal stem cells in mice

Gene. 2021 Apr 5:775:145447. doi: 10.1016/j.gene.2021.145447. Epub 2021 Jan 19.

Authors

Zhi Hou Guo¹, Yang Yan Sheng Jia², Yi Ming Zeng³, Zhao Fa Li², Jun Sheng Lin⁴

Affiliations

¹ School of Medicine, Huaqiao University, Quanzhou, Fujian 362021, China; Stem Cell Laboratory, The Second Affiliated Hospital of Fujian Medical University, China.
² School of Medicine, Huaqiao University, Quanzhou, Fujian 362021, China.
³ The Second Affiliated Hospital of Fujian Medical University, China.
⁴ School of Medicine, Huaqiao University, Quanzhou, Fujian 362021, China. Electronic address: junshenglin@hqu.edu.cn.

PMID: 33482278
DOI: 10.1016/j.gene.2021.145447

Abstract

Limbal stem cells (LSCs) reside in the basal layer of limbal epithelial cells (LECs). They are crucial for maintenance of corneal epithelium homeostasis and corneal wound healing. Their stemness is determined by their gene expression pattern. Despite of several positive identifiers have been reported, the unique biomarker for LSCs still remain elusive. Differentially expressed genes (DEGs) between stem cells and differentiated cells affect the fate of stem cells via specific signaling pathway. In order to understand the DEGs in the LSCs, RNA-seq was firstly conducted using a mouse model. A total of 1907 up-regulated DEGs and 395 down-regulated DEGs were identified in the limbus (L) compared to central cornea (CC) and conjunctiva (Cj). Reliability of the expression of genes from RNA-seq analysis was evaluated by quantitative real-time polymerase chain reaction (qRT-PCR) and immunofluorescence staining. The expression pattern of putative biomarkers was considered to be age-related. In up-regulated DEGs GO analysis, 570 gene ontology (GO) terms were significantly enriched. Five groups of genes related with biological processes from these significantly enriched GO terms comprised ionic transport, regulation of tissue development, muscle contraction, visual perception, and cell adhesion, which were clustered as a weighted similar network. Whereas, in down-regulated DEGs GO analysis, 61 GO terms were significantly enriched and only one group of ATP biosynthesis and metabolic process were clustered. Furthermore, we identified 55 signaling pathways by the Kyoto Encyclopedia of Genes and Genomes (KEGG) database based on up-regulated genes and 14 KEGG pathways based on down-regulated genes. In this study, we provide a landscape of the expression of putative LSCs biomarkers and stemness-related signaling pathways in a mouse model. Our findings could aid in the identification of LSC niche factors that may be related to the stemness of the LSCs.

Keywords: Differentially expressed genes; Limbal stem cells; RNA-seq; Stemness.

MeSH terms

Animals
Cells, Cultured
Conjunctiva / chemistry
Epithelium, Corneal / chemistry*
Gene Expression Profiling / veterinary*
Gene Expression Regulation
Gene Regulatory Networks*
High-Throughput Nucleotide Sequencing
Mice
Protein Interaction Maps
Sequence Analysis, RNA
Stem Cells / chemistry