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Whole Mount Immunofluorescent Staining of the Neonatal Mouse Retina to Investigate Angiogenesis In vivo
Published on: July 9, 2013
Multiple Hub Genes as Diagnostic and Therapeutic Targets Inducing Inflammation and Angiogenesis in Retinopathy of
Cheng Du1, Yuan Tian2, Yu Liu2
1Jiaxing Hospital of Traditional Chinese Medicine, Zhejiang Chinese Medical University, Jiaxing, Zhejiang Province, 314001, People's Republic of China.
Introduction:
The pathogenesis of retinopathy of prematurity (ROP) is intricate and multifactorial. The current treatments for ROP include laser photocoagulation, cryotherapy, scleral buckling or vitrectomy and anti-VEGF drugs, yet which have numerous adverse effects. Consequently, the objective of this investigation was to mine new biomarkers of ROP and identify potential therapeutics that target these biomarkers.
Methods:
GSE130400, the expression profile of ROP, was downloaded from the GEO database and annotated by dplyr package in R. The limma package was employed to identify differentially expressed genes (DEGs) between cases and controls. WGCNA was utilized to obtain oxygen-induced retinopathy (OIR)-related modules, and then key genes were obtained in the intersection of DEGs and the above modules. Biological functions and pathways of key genes were enriched through DAVID, Metascape and Gene set enrichment analysis. Hub genes were screened by three machine learning methods and validated by nomograms, ROC curves and qRT-PCR. CIBERSORT was used to estimate the abundances of immune cells and Pearson analysis revealed immune cells, checkpoints and chemokines associated with hub genes. Finally, we constructed a ceRNA network and a drug-gene interaction network.
Results:
Utilizing GSE130400 as a basis, a total of 798 DEGs and 3711 genes from three OIR-related modules in WGCNA were identified, resulting in the identification of 681 key genes. Hub genes Plxnd1, Esm1 and Cd248 were explored using various machine learning methods and proved to be closely related with the occurrence of ROP through nomograms, ROC curves and qRT-PCR. Enrichment analysis revealed a significant enrichment of hub genes in processes related to endothelial cell proliferation, migration, and angiogenesis, among others. Immune analysis displayed that the development of ROP was associated with alterations in M0 macrophages and M2 macrophages, with hub genes participating in the regulation of immune cells M0 macrophages, Th2 cells, and NK resting cells, as well as chemokines lncRNA H19 (H19), CXCR5 (F5), CCL27 (F7) and CCL2 (C2). Furthermore, the drug-gene interaction network displayed 14 possible candidate drugs targeting 3 hub genes.
Conclusion:
Plxnd1, Esm1 and Cd248 might play significant roles in the progression of ROP and could become possible diagnostic and therapeutic targets in ROP.
Insights
Researchers identified Plxnd1, Esm1, and Cd248 as key genes in retinopathy of prematurity (ROP) pathogenesis. These genes may serve as novel diagnostic and therapeutic targets for ROP, offering potential alternatives to current treatments.
Area of Science:
- Ophthalmology
- Genetics
- Immunology
Background:
- Retinopathy of prematurity (ROP) pathogenesis is complex and multifactorial.
- Current ROP treatments have significant adverse effects.
- There is a need for novel biomarkers and targeted therapeutics for ROP.
Purpose of the Study:
- To identify novel biomarkers for retinopathy of prematurity (ROP).
- To discover potential therapeutic targets for ROP based on identified biomarkers.
Main Methods:
- Utilized gene expression data (GSE130400) and differential gene expression analysis.
- Employed Weighted Gene Co-expression Network Analysis (WGCNA) to identify key genes.
- Validated hub genes (Plxnd1, Esm1, Cd248) using machine learning, nomograms, ROC curves, and qRT-PCR.
Main Results:
- Identified 681 key genes, including hub genes Plxnd1, Esm1, and Cd248, associated with ROP.
- Enrichment analysis revealed hub genes' involvement in angiogenesis and endothelial cell functions.
- Immune analysis indicated associations with M0 and M2 macrophages, Th2 cells, NK resting cells, and specific chemokines.
Conclusions:
- Plxnd1, Esm1, and Cd248 are significantly implicated in ROP progression.
- These hub genes represent promising diagnostic and therapeutic targets for ROP.
- Identified 14 potential drugs targeting the identified hub genes.
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