Analysis of shared ceRNA networks and related-hub genes in rats with primary and secondary photoreceptor degeneration
Jia Liang1, Dong Fang1, Fei Yao1
1Shenzhen Eye Hospital, Shenzhen Eye Institute, Jinan University, Shenzhen, Guangdong, China.
Introduction:
Photoreceptor degenerative diseases are characterized by the progressive death of photoreceptor cells, resulting in irreversible visual impairment. However, the role of competing endogenous RNA (ceRNA) in photoreceptor degeneration is unclear. We aimed to explore the shared ceRNA regulation network and potential molecular mechanisms between primary and secondary photoreceptor degenerations.
Methods:
We established animal models for both types of photoreceptor degenerations and conducted retina RNA sequencing to identify shared differentially expressed long non-coding RNAs (lncRNAs), microRNAs (miRNAs), and messenger RNAs (mRNAs). Using ceRNA regulatory principles, we constructed a shared ceRNA network and performed function enrichment and protein-protein interaction (PPI) analyses to identify hub genes and key pathways. Immune cell infiltration and drug-gene interaction analyses were conducted, and hub gene expression was validated by quantitative real-time polymerase chain reaction (qRT-PCR).
Results:
We identified 37 shared differentially expressed lncRNAs, 34 miRNAs, and 247 mRNAs and constructed a ceRNA network consisting of 3 lncRNAs, 5 miRNAs, and 109 mRNAs. Furthermore, we examined 109 common differentially expressed genes (DEGs) through functional annotation, PPI analysis, and regulatory network analysis. We discovered that these diseases shared the complement and coagulation cascades pathway. Eight hub genes were identified and enriched in the immune system process. Immune infiltration analysis revealed increased T cells and decreased B cells in both photoreceptor degenerations. The expression of hub genes was closely associated with the quantities of immune cell types. Additionally, we identified 7 immune therapeutical drugs that target the hub genes.
Discussion:
Our findings provide new insights and directions for understanding the common mechanisms underlying the development of photoreceptor degeneration. The hub genes and related ceRNA networks we identified may offer new perspectives for elucidating the mechanisms and hold promise for the development of innovative treatment strategies.
Insights
This study reveals shared molecular mechanisms in photoreceptor degenerative diseases, identifying key genes and pathways involved in immune responses. These findings offer potential targets for novel therapeutic strategies to combat vision loss.
Area of Science:
- Ophthalmology
- Molecular Biology
- Genetics
Background:
- Photoreceptor degenerative diseases cause irreversible vision loss.
- The role of competing endogenous RNA (ceRNA) networks in these diseases is not well understood.
- Exploring shared ceRNA mechanisms could reveal common pathways in primary and secondary photoreceptor degenerations.
Purpose of the Study:
- To investigate the shared ceRNA regulatory network in primary and secondary photoreceptor degenerations.
- To identify common molecular mechanisms and potential therapeutic targets.
- To explore the role of immune cell infiltration in these diseases.
Main Methods:
- Established animal models for photoreceptor degenerations.
- Performed retina RNA sequencing to identify differentially expressed long non-coding RNAs (lncRNAs), microRNAs (miRNAs), and messenger RNAs (mRNAs).
- Constructed a shared ceRNA network, performed functional enrichment, protein-protein interaction (PPI) analysis, and immune cell infiltration analysis.
Main Results:
- Identified a shared ceRNA network involving 3 lncRNAs, 5 miRNAs, and 109 mRNAs.
- Discovered the complement and coagulation cascades pathway as common to both disease types.
- Identified eight hub genes enriched in immune processes, with altered T and B cell infiltration, and potential drug targets.
Conclusions:
- The study elucidates common molecular mechanisms underlying photoreceptor degeneration.
- Identified hub genes and ceRNA networks provide novel insights into disease pathogenesis.
- These findings may pave the way for innovative therapeutic strategies for vision-threatening diseases.
