Identification of a novel ferroptosis-related gene signature associated with retinal degeneration induced by light damage in mice

Xin-Lan Lei; Qiao-Li Yang; Yong-Zhao Wei; Xu Qiu; Hui-Yi Zeng; Ai-Min Yan; Kai Peng; Ying-Lin Li; Feng-Qin Rao; Feng-Hua Chen; Lue Xiang; Kun-Chao Wu

doi:10.1016/j.heliyon.2023.e23002

Identification of a novel ferroptosis-related gene signature associated with retinal degeneration induced by light damage in mice

Heliyon. 2023 Nov 30;9(12):e23002. doi: 10.1016/j.heliyon.2023.e23002. eCollection 2023 Dec.

Authors

Xin-Lan Lei^{1

2}, Qiao-Li Yang³, Yong-Zhao Wei¹, Xu Qiu¹, Hui-Yi Zeng³, Ai-Min Yan¹, Kai Peng¹, Ying-Lin Li¹, Feng-Qin Rao³, Feng-Hua Chen¹, Lue Xiang³, Kun-Chao Wu^{1

3}

Affiliations

¹ The Department of Ophthalmology, First People's Hospital of Guiyang, Guiyang, China.
² Aier Eye Hospital of Wuhan University, Wuhan, China.
³ State Key Laboratory of Ophthalmology, Optometry and Vision Science, Eye Hospital, Wenzhou Medical University, Wenzhou, China.

Abstract

Background: Neurodegenerative retinal diseases such as retinitis pigmentosa are serious disorders that may cause irreversible visual impairment. Ferroptosis is a novel type of programmed cell death, and the involvement of ferroptosis in retinal degeneration is still unclear. This study aimed to investigate the related ferroptosis genes in a mice model of retinal degeneration induced by light damage.

Methods: A public dataset of GSE10528 deriving from the Gene Expression Omnibus database was analyzed to identify the differentially expressed genes (DEGs). Gene set enrichment analysis between light damage and control group was conducted. The differentially expressed ferroptosis-related genes (DE-FRGs) were subsequently identified by intersecting the DEGs with a ferroptosis genes dataset retrieved from the FerrDb database. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were further performed using the DE-FRGs. A protein-protein interaction (PPI) network was constructed to identify hub ferroptosis-related genes (HFRGs). The microRNAs (miRNAs)-HFRGs, transcription factors (TFs)-HFRGs networks as well as target drugs potentially interacting with HFRGs were analyzed utilizing bioinformatics algorithms.

Results: A total of 932 DEGs were identified between the light damage and control group. Among these, 25 genes were associated with ferroptosis. GO and KEGG analyses revealed that these DE-FRGs were mainly enriched in apoptotic signaling pathway, response to oxidative stress and autophagy, ferroptosis, necroptosis and cytosolic DNA-sensing pathway. Through PPI network analysis, six hub ferroptosis-related genes (Jun, Stat3, Hmox1, Atf3, Hspa5 and Ripk1) were ultimately identified. All of them were upregulated in light damage retinas, as verified by the GSE146176 dataset. Bioinformatics analyses predicated that 116 miRNAs, 23 TFs and several potential therapeutic compounds might interact with the identified HFRGs.

Conclusion: Our study may provide novel potential biomarkers, therapeutic targets and new insights into the ferroptosis landscape in retinal neurodegenerative diseases.

Keywords: Ferroptosis; Hmox1; Light damage; Photoreceptor; Retinal degeneration; Stat3.